The intermittent issue you are seeing might have been caused by network issues when git took long time to checkout the source code. Usually happens when network is crappy or the repo you are trying to clone is really big one.
Possible solutions you should try:
1> Better to use ssh than https to checkout the source code from git.
For more details on using ssh with git checkout : https://confluence.atlassian.com/display/BAMBOO/Git
2> Use shallow clones in checkout source task, ( if you don't need the tags it better to use shallow clones they are faster)
A snapshot on where : https://confluence.atlassian.com/display/BAMBOO/Bitbucket?focusedCommentId=600867102#comment-600867102
Use shallow clones | Allows Bamboo to perform shallow clones (i.e. history truncated to a specified number of revisions). This should increase the speed of the initial code checkouts, however if your build depends on the full repository history, we recommend that you do not use this option. Shallow clones are enabled by default. |
3> set up linked source repositories
Details : https://confluence.atlassian.com/display/BAMBOO/Linking+to+source+code+repositories
Specific to bit bucket : https://confluence.atlassian.com/display/BAMBOO/Bitbucket
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