The only thing I've felt was a problem is that on Anderson lowers you have to use a shorter grip screw.
If you know that ahead of time then you're prepared and you have the shorter grip screw already in hand and it doesn't come as a surprise. If it comes at a surprise and the build has to wait until you can either go get one at a local gun shop or you order one and the thing arrives in the mail. That's a pain in the ass.
On a thread on a different forum several posters stated that this was no longer an issue and that all the new Anderson lowers use a standard grip screw. I haven't confirmed that myself and the Anderson lowers I've built guns off of were a couple years old.
That shorter grip screw is the only issue I've run into and I've assembled a fairly wide array of lowers (1 Noveske, 7 PSA, 1 Superior Arms, 2 RRA, 1 CY6 and 2 Anderson).
In my experience Anderson works fine.