My program depends on two libraries. The first one uses scons and the last one uses qmake. The program itself uses scons. So to build the whole project, I have a makefile that builds the first library with scons and the second library with qmake.
Is it considered bad practice to use multiple build tools on the same project? Should I create a scons-file to build the last library too?
I wouldn't say so. On complex projects it's common for source to come from several different source control systems (I think I read somewhere that the Chromium project references something like 7 different repositories). Projects grow and have quirks of history that mean different parts may be grafted on over time, contributed by different people with different backgrounds.
If it looks like it might be trivial to convert the project to use scons then do that. If it looks any more complicated than that then it may be worth sticking with what you've got. If you find that maintaining the qmake system becomes a time-sink then it may be worth investing the time in migrating to scons.
Think of it in economic terms: if it's not taking time or effort to maintain then leave it as is. If it is taking time to maintain, consider if it would actually take longer to migrate to something else. Don't forget the xkcd classic: