Firstly, you can set the ships speed while launching. Adding this ifcheck fixes that.
if( ship->shipstate == SHIP_LAUNCH || ship->shipstate == SHIP_LAUNCH_2)
send_to_char( "&RYou can't do that until after you've left the atmosphere!\r\n", ch );
Secondly, you can set the ships speed to the same speed over and over. This isn't per se a bug, but it is a nuisance and commonly abused.
In space.c do_accelerate, find:
change = atoi( argument );
if( change == ship->currspeed )
send_to_char( "&RThe ship is already going that speed.\r\n", ch );
Will have to check in a bit to see if this is applicable to SWFotE