What you had wasn't trouble but conflicts. This happens when the files are modified by two different persons at the same place (you both add/remove/modify things inside the same lines).
You can simply update your files manually, by deciding to keep everything between <<<<<<< HEAD
and =======
, or between =======
and >>>>>>>
, or some mix of the two. Once you resolve all your conflicts, you just need to commit your changes.
To discard local changes on a file, you can do
git checkout yourfile
or, for all files using
git checkout -- .
You can also decide, for each file, if you want to keep your version or the repository version with
git checkout --ours yourfile # Your version
git checkout --theirs yourfile # Repository version