If I can be so bold and extrapolate my findings,I would say that this isn't a WINE/Linux specific issue.
I've had the exact same crash on Windows 7 weeks ago with 1.0 version of Xenonauts. Crash while disabling missiles on a second interceptor.
And I have same software (OS, WINE, Xenonauts) on my second Linux machine, but it isn't crashing.
So I would say it is probably a system specific issue.