Not a bug. QB64 is a compiler, not an interpreter. You make stand alone EXE files with it, rather than running them inside the IDE.
Due to this change, you can't use RUN with *.BAS files in QB64, as your compiled program wouldn't have a clue what the heck to do with that BAS format. Instead, compile "INPUT.BAS" to it's executable, and then you should be able to either RUN, or SHELL out to "INPUT.EXE".