Seen this problem again in 2019.1, had same problem a couple of years ago - https://intellij-support.jetbrains.com/hc/en-us/community/posts/360000098179-Git-status-sometimes-not-showing-correct-branch
Using phpstorm 2019.1 on Mac. GitKraken is the primary git client. When changing branches in GitKraken, phpstorm doesn't notice this (files aren't update or the name of the branch in the lower right corner) until I right-click on the project and choose Synchronize. Closing and re-opening the project also solves this.
Running "git status" in the terminal window of the project shows correct branch.
Phpstorm 2018.3 worked without a flaw.