You can force Unity to serialise assets and scenes as YAML text based files, this should resolve your merge issues with Git. This setting can be found under the Edit > Project Settings > Editor menu. You then set the "Asset Serialization" setting to Force Text, this will allow you to merge scenes using Unity's YAMLMerge.

Be warned, depending on the project size when changing this setting re-importing everything can take hours, and it has to be done on every client. There are other additional measures you can take to improve your workflow with Unity and Git, I'd recommend looking at this excellent post by David Douglas which goes into much more depth and teaches some of the ways you can all work on the same scene and merge your changes once you're all at your milestones.
There's also this good Unity Answers post that talks about the Pros and Cons of different asset serialisation methods that you might want to take a look at before committing to any of them.