Understanding Issues, Causes and Solutions in Open-Source LLM-based Multi-Agent Systems

cs.SE cs.AI Asad Ur Rehman, Syed Mohammad Kashif, Ruiyin Li, Peng Liang, Zengyang Li, Arif Ali Khan · Oct 1, 2026
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What it does
The paper mines 22,848 closed GitHub issues from 21 open-source LLM-based multi-agent systems, filtering down to 944 MAS-related reports to catalog what goes wrong in practice. Through qualitative coding, the authors map issues, causes,...
Why it matters
Through qualitative coding, the authors map issues, causes, and solutions, finding that orchestration and workflow design dominate practitioner pain points. It matters because it replaces anecdotal MAS debugging lore with an empirical...
Main concern
The paper delivers a descriptively rich taxonomy of practitioner-reported issues, causes, and solutions in open-source LLM-based multi-agent systems. However, its reliability is weakened by a filtering pipeline that relies on a single...
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Plain-language introduction

The paper mines 22,848 closed GitHub issues from 21 open-source LLM-based multi-agent systems, filtering down to 944 MAS-related reports to catalog what goes wrong in practice. Through qualitative coding, the authors map issues, causes, and solutions, finding that orchestration and workflow design dominate practitioner pain points. It matters because it replaces anecdotal MAS debugging lore with an empirical taxonomy grounded in actual maintenance traces.

Critical review
Verdict
Bottom line

The paper delivers a descriptively rich taxonomy of practitioner-reported issues, causes, and solutions in open-source LLM-based multi-agent systems. However, its reliability is weakened by a filtering pipeline that relies on a single local LLM evaluation followed by first-author manual curation without independent double-coding for the full set, and by the fact that extracted solutions are treated as effective without outcome validation. The taxonomies are plausible and useful as heuristic catalogs, but should be read as observational mappings rather than rigorous causal findings.

“Inter-rater agreement between the two authors was measured using Cohen's Kappa coefficient (Cohen, 1960), yielding a value of 0.82, which indicates a very high level of labeling consistency between the two authors.”
Rehman et al. · Section 2.3.1
“Finally, 944 out of the 22,848 closed issues were considered real multi-agent issues.”
Rehman et al. · Section 2.3.2
What holds up

The authors collect a large initial corpus and apply transparent inclusion criteria to select 21 active, popular projects, which lends breadth to the sample. The resulting taxonomies are granular and well-illustrated with direct practitioner quotes, and the issue-cause-solution mappings offer a structured lens for framework developers. Notably, the prominence of Orchestration & Execution Issue and Optimize Workflow aligns with known coordination bottlenecks in multi-agent systems, giving the taxonomies face validity.

“The largest category among all issues is Orchestration & Execution Issue. 54.8% of these issues are associated with identified causes, and the most frequent causes are Workflow Problem (WP) (65), Agent Lifecycle Problem (ALP) (10), and Integration Problem (IP) (9).”
Rehman et al. · Section 3.2.2
“We prioritized projects with recent commit activity to ensure they reflect current MAS practices, and we manually verified whether each project explicitly described multi-agent collaboration rather than single-agent LLM usage.”
Rehman et al. · Section 2.2
Main concerns

The study conflates issue frequency with importance by treating all issues equally regardless of project scale, so 77 CrewAI issues and 6 ChatDev issues carry the same analytic weight despite vastly different user bases. Category boundaries are also blurry: Context Loss appears under both Orchestration & Execution Issue and Memory & State Management Issue with overlapping definitions, suggesting the taxonomy may not be mutually exclusive. Moreover, analyzing only closed issues systematically excludes unresolved and potentially severe open problems, biasing findings toward more tractable failures and away from deep architectural defects.

“The remaining categories each account for less than 10%, including Tool Issue (9.2%), Integration Issue (6.7%), Role Issue (3.8%), Environment & Configuration Issue (3.5%), Output Issue (3.1%), Documentation Issue (2.8%), Communication Issue (2.6%), Performance Issue (2.0%), Model Issue (1.6%), Compatibility Issue (1.4%), Error Handling Issue (1.3%), Task Management Issue (1.2%), and Security Issue (0.3%).”
Rehman et al. · Section 3.1
“In some cases, the discussion was too vague to identify specific causes or solutions, while in others, issues were automatically closed due to inactivity, low priority, or high complexity, making it difficult to extract information.”
Rehman et al. · Section 2.4.2
Evidence and comparison

The evidence supports descriptive claims about commonly discussed pain points, but the paper never establishes a counterfactual—there is no comparison against single-agent LLM systems or traditional non-LLM multi-agent codebases—so it remains unclear which problems are distinctive to LLM-based MAS. The authors assert a lack of prior empirical studies in this space, yet they do not systematically map their taxonomy onto existing software engineering defect classifications to demonstrate novelty. Consequently, many categories (e.g., Dependency Conflict, Parameter Configuration Error) read as generic software engineering issues recast in agent terminology.

“Despite the rapid adoption and significant potential of LLM-based MAS (Guo et al., 2024), there remains a lack of empirical studies regarding the challenges associated with their development and maintenance in real-world contexts.”
Rehman et al. · Section 1
“We collected closed issues from 21 open-source LLM-based MAS and observed that not all reported issues were relevant to MAS-related problems.”
Rehman et al. · Section 2.3
Reproducibility

Reproduction is hampered by missing artifacts: the DeepSeek-R1 prompts, temperature settings, and Ollama configuration are not disclosed, and the MS Excel dataset is referenced but not linked or archived in the paper text. The formal extraction was performed by a single author with post-hoc review rather than independent parallel coding, and inter-rater reliability is reported only for a 500-issue pilot, not for the final 944-issue taxonomies. Because GitHub issue trackers evolve continuously, the lack of versioned issue dumps or permanent identifiers for the analyzed issues makes independent replication nearly impossible.

“We randomly selected 500 issues from the collected 22,848 closed issues and processed them with the DeepSeek-R1 model deployed locally via Ollama, with carefully crafted prompt instructions and iterative refinement to identify MAS-related issues (Montes et al., 2025).”
Rehman et al. · Section 2.3.1
“The results of the formal data filtering were compiled and recorded in MS Excel files (Rehman et al., 2026).”
Rehman et al. · Section 2.3.2
Abstract

With the advancement of LLM-based multi-agent systems (MAS), an increasing number of opensource projects are adopting multi-agent architectures as the foundation of their core functionality. Although research and practice on MAS have attracted considerable attention, limited studies have explored the challenges faced by practitioners of open-source LLM-based MAS, the causes of these challenges, and potential solutions. To address this gap,we conducted an empirical study to understand the issues that practitioners encounter when developing and using open-source LLM-based MAS, the possible causes of these issues, and potential solutions. We collected 22,848 closed issues from 21 open-source LLM-basedMASand applied a mixed automated and manual filtering approach to reduce the dataset to 944 issues related to LLM-based MAS.We then analyzed these issues to understand the frequent issues encountered by practitioners, their underlying causes, and potential solutions. Our study results show that (1) Orchestration & Execution Issue is the most common issue faced by practitioners, (2) Workflow Problem, Tool Integration Problem, and Memory Problem are identified as the most frequent causes of the issues, and (3) Optimize Workflow is the predominant solution to the issues. Based on the study results, we derive empirically grounded implications for practitioners and researchers aimed at improving orchestration, tool integration, and memory mechanisms in LLM-based MAS.

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