ATmega16HVB stack pointer does not intialize correctly and must be initialized by application. This is an issue with the actual chip and the simulator just reflects reality, see data sheet Errata section 38.1.1 (Rev. B).
ATmega169PA/165PA/329P/325P/3250P/3290P/649P/645P/6490P/6450P watchdog timer does not work (#9301)
System clock prescaler not included in simulator models, writing
CLKPR
will not affect system clock.
External interrupt flank rising flank on some mega devices triggers on both flanks (#13434)
CLKPR
is not updated when debugging if CKDIV8
fuse
is programmed (#10515)