Hi,
I used to work in an environment where we used uncrustify [1] to check formatting during CI time (github + jenkins iirc).
In general it worked quite well but sometimes indeed it did some unexpected stuff.
So I'd say I'm not for or against using this kind of tooling during CI to check formatting. It has good stuff (avoid adding whitespace artifacts and bad formatting), but on the other side it has issues (more time spent on formatting, sometimes it adds its own formatting artifacts).
Furthermore, that means probably we need to run it once over all the code base and submit patches to fix it so we can then use it as a base to check the changes.
[1] http://uncrustify.sourceforge.net/