If the application doesn’t crash after the error, perhaps look in/proc/$pid/maps to check what libraries have been mapped into the application. A command like the following might help:
cat /proc/$pid/maps | awk '{print $6}' | sort | uniq
GTK registers classes at runtime in a global namespace, so my hunch is that you’ve some how got two copies of GTK mapped into your application (the warning is about the GtkIMContext class itself, rather than a subclass that would belong to one of the input method modules).
If that is the case, can you share the paths of the two libraries? That should help in narrowing down what’s going on.