A merge conflict in the context of Bitcoin occurs when two branches have made conflicting changes to the same code, and the version control system cannot automatically determine which change is correct.
For example, if one developer modifies a certain function in Bitcoin Core while another modifies the same function in a Bitcoin sidechain platform like Elements (which Liquid is an implementation of). This requires manual review to ensure that the final Elements codebase is consistent, functional, and compatible with its Bitcoin Core counterpart.
Merge conflicts are common in open-source projects like Bitcoin (and it's second-layer protocols) that have an independent, distributed network of developers. Good communication is key.