Strange behavior. tasks+git

I'm using YouTrack + Git;

When I opening some task (Ctrl+Shift+N) and writing code. When I'm closing the task, I set check in the dialog window - Commit in git. But Storm commit just one file and other chenged files moved in other changelist, which i open after.

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Please try Tools -> Tasks & Contexts -> Open Task.
Will it work for you?

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Yes.

I do:

1)  Open Task #1 (for example)
2)  edit some code in some files
3)  Close Task #1 - set check: commit, merge branch and close issue
4)  Open Task #2
5)  edit some code
6)  close task #2 - set check: commit, merge branch and close issue

After i'm looking in SourceTree (GUI for git);  There is Task #1 commited just 1 file and second task commited too. But some files from task #1 acommited in task #2. Or it is stay like not fixed changes.

But also i have problems when i change tasks and Storm is merging branches after it try delete my Master brunch and show me "Error: Can't delete Master branch..."

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