The holes in de PCB are exactly aligned with the ones in the pump, but since the thread in the pump is so minimal, sometimes the studs tent to tilt very slightly (e.g. if the washers aren't perfectly seated): on the topside this quickly makes a mm difference. Even that is usually not a problem, if you don't tighten 1 screw first, and then try to get in the other screw (which you should never do mounting anything; always get all bolts and screws in, then tighten them).
I haven't seen it as extreme is this, and I have done many myself... but for everything there is a first time :-).
Thanks for the pictures, and indeed a good tip: Everything SHOULD fit without force or bending anything... IF not, have a close look, are the studs nicely parallel etc.