Why Git Says You Have Merge Conflicts You Didn’t Cause And What’s Actually Happening

A practical debugging guide for understanding and resolving Git merge conflicts that appear in files you didn’t intentionally change.

You pull a branch.
Git reports merge conflicts.

The files listed:

• Don’t look familiar
• Weren’t intentionally changed
• Sometimes weren’t even opened by you

This guide explains why that happens and how to resolve it safely.

Most “mystery” merge conflicts aren’t caused by mistakes. They’re caused by formatting tools, rewritten history, generated files, or indirect changes that Git can’t automatically reconcile.

This guide breaks down what Git is actually comparing, why it flags conflicts that feel wrong, and how to fix them without guessing or making things worse.

What this guide covers

• Why Git reports conflicts even when you didn’t edit the file
• How formatters and tooling create hidden conflicts
• Line ending issues and why they affect entire files
• Rebase and history rewrite side effects
• How to safely read and resolve conflict markers
• A step-by-step checklist for resolving conflicts cleanly
• How to prevent the same conflicts from recurring

What this guide is NOT

• Not a Git tutorial
• Not a list of commands without context
• Not “just pick theirs and move on” advice

This is a focused troubleshooting guide for understanding and resolving merge conflicts with confidence.

Who this is for

• Developers confused by unexpected merge conflicts
• Anyone working on shared branches or teams
• Developers using formatters, linters, or auto-generated files
• Anyone tired of treating Git conflicts like a guessing game

Format

• PDF
• Clean, skimmable layout
• Checklist-driven
• Easy to reference while resolving conflicts

If merge conflicts regularly slow you down or make you nervous to proceed, this guide will save you time and stress.

What You’ll Learn

• Why Git flags conflicts you didn’t intentionally cause
• How formatters and tooling create hidden conflicts
• How line endings and history rewrites affect merges
• How to safely read and resolve conflict markers
• When to keep yours, theirs, or combine changes
• How to reduce merge conflicts going forward