Since you are not pushing commits too fast or anything, there must be some content that triggers Travis’ heuristics.
As such, you need to find out which commit first triggered the check.
This goes earlier in history than https://travis-ci.org/lingthio/Flask-User/requests has saved but the last build is for https://github.com/lingthio/Flask-User/commit/ae9cbcd38705d59e81a23f95de8ee61239c5a468. So the faulty change must be between that and the next commit that would have triggered a build.
There may also have been a change in Travis project settings (e.g. new envvars) that tips the detection off.
I deduce that by the fact that PR builds go successfully, and they don’t have access to secret variables.