We recently ran across a sticky situation related to the drill size for a thru-hole part. Most of what we do is machine SMT work, but most boards have one or two thru-hole parts on them as well. Occasionally, we get boards with a lot or even all thru-hole.
Just the other day, we got one in that, in total for the job, had several hundred thru-hole resistors. This wouldn't be an issue at all except that the hole size was just a little bit too small for the leads. In almost all cases, there pretty much isn't anything we can do in a case like that other than send the boards back to the customer to be remade. These were customer supplied, so as much as we hate to do it, it was all on their dime and we still had to charge for the labor that we had already put into the project.
This customer was using Protel. I had the same thing happen to me some time ago with a board I laid out in Eagle. It was a PIC micro board designed to run a couple of motor driver boards. After getting the boards fabbed, I started to assemble them and discovered that none of my Molex keyed connector blocks would fit. The drilled holes were too small.
At first, I was upset with the board house, but when I went back into Eagle and looked a little closer, something didn't look right. I thought that I had used the correct parts library - and upon double-checking found that I had - but the holes sizes used on the package were too small.
Looking at my board (click image to enlarge), "A" shows the spot for the three-pin Molex connector. Comparing the hole size for that, look closely and you can see in my call-outs that the holes are the same size as the holes for IC1 (call out C) and are slightly smaller than the holes for my breakaway connectors (call outs B and D).
The drill size used for the Molex connectors in the library package in Eagle was .032 while the datasheet specifies a .040 hole size. That's not gonna work. The breakaway connectors call for a .045 inch hole size while the library package used a hole size of .036. Oddly, because of drill size variation, I could wiggle the breakaway connectors in.
In both cases, the real solution was to modify the parts libraries to increase the hole size. These may have been user created libraries or they may have came with the original install. I don't know for sure, but with so many new components coming out, it's quite likely that you'll have to use custom libraries no matter what CAD package you are using.
What should you do?
It's always a good idea to look at things like footprint, SMT pad size and thru-hole hole size in your design check - especially if you are using third-party libraries. I didn't really pay much attention to that while originally laying it out, but once I went back in to check it out, it was obvious at a glance. An extra few minutes spent looking at those things would have saved me (and this recent customer) a lot of time and money