Cranks and spindles are built to produce a chainline, not match a derailleur. The derailleurs are also built to go to a chainline, not for a particular crank.

If anything, your bike is a road bike and the crank is an MTB crank, so it may be further out rather than further in. Did you get a BB for a 68mm shell or a 73mm?

And 3.5mm is a fair amount for crank chainline. But there could always be a problem with your derailleur, too.