I don't know if things have changed recently but at Qt at least used to require custom C++ extensions. This requires you to use custom toolchains or the recommended way of using the Qt Creator IDE. This isn't necessarily bad (I've only quickly tried it out, I don't really know) but it certainly makes me look at other alternatives first.
This isn't perhaps a big problem if you use other languages than C++ and there are decent wrappers available. But having to use a custom compiler/preprocessor just to get a GUI up isn't what I really want.
Qt is a pretty intrusive framework and ecosystem, where you have QStrings and QSockets and QEverything. GTK is perhaps a bit more lean and mean library than a full ecosystem.
I've also noticed that Qt applications do not work very well over remote X connection over slow networks. Apps built with other GUI toolkits work much more fluently. (I understand that this is not very common these days but I still do work on remote X on a daily basis).
I am sure that the Qt frameworks solve practical problems in cross platform development, but I'd rather not get involved in a whole ecosystem when all I need is a GUI toolkit.