I really dislike it when they merge universes that were clearly originally separate, causing all sorts of problems.It's super rare, but off the top of my head I can think of Richard Belzer appearing as NBC's Munch on both HBO's The Wire and Fox's The X-Files, which could mean they all exist in the same shared universe.
This is why Marvel and DC have shared universes, which they originally did not, and it leaves one to wonder why Batman isn't calling Superman to fix most of the problems he faces in a second.
But then again, Superman is known to not use his “super speed” when it could solve many problems.