Lot's of types of components can cause footprint woes. QFNs have their center pad issues. BGAs have escape via issues. But the most common footprint issues seem to be with connectors. At least with chips and discrete silicon and passive components most manufacturers pretty much follow IPC standard footprints. Sometimes they'll create new ones for smaller parts, but generally they still stay reasonably close to in line.
Connectors are another story though. I'm not sure any manufacturer follows anything close to a standard. This pair of ethernet jacks is a good example. Often the actual pin layout will match, but the mounting will vary widely. I've seen it on ethernet, mini-USB, micro-USB and even the old, old RS232 connector.
It gets more frustrating when they're almost the same. We see that a lot; the layout will almost, but not quite match a footprint in the library. The bottom line is never take a connector footprint for granted. Always double check before getting your boards fabbed.
Carburetors man. That's what life is all about.