So, my tip to myself and others is to keep that female part attached to your machine, until you have checked the fit with the mating part. It is certainly much easier to recut a fit dimension on the machine than to do it by hand.
How do you address this issue?
Our good friend Tim Merrill has always advised this - i.e., cutting the male part first, then cut the female part, keeping the female part attached to your spoilboard to check the fit of the two. If the male part fits too tightly, then you can easily modify your original file, then recut the female pocket/dado/slot by a tiny offset amount until it does. This is just one of the many, many golden nugget
tips I've/we've learned from him.
Another great tip is one I learned from Gary Campbell for determining if, or by how much, an End Mill bit is undersize. He recommends performing a plunge cut (drill) or slot cut with say, your 0.25" EM in some scrap and measuring the HOLE (or SLOT width) itself. The size of the real-world cut is often a better determinant than just measuring the bit alone.