Why is TC so eager to use 'earlier commit' instead of head

We're using teamcity with git, checkout rules, and pull request verification (bitbucket).

Quite often we get into problems with the pullrequest checks since TeamCity calculates that a parent commit is sufficient according to the checkout rules and builds that commit instead of e.g. a merge into the pull request branch.

This leads to a situation in bitbucket that the pullrequest doesn't pass build verification since the latest commit / branch-head (usually a merge) in the branch isn't built.

Yes, 'build-wise' given the checkout rules the selected commit is fine. It's the same code as head but integration between systems does not work.

We have the 'Trigger a build on each check-in' unchecked.
No reason to build every commit on a push but branch head should be selected.

( I also find it unnatural that different packages built by our ci are done on different git-shas though they see the same repo, branches and commits )

I know that there are alot of discussions regarding too many builds, I see the opposite.