Greetings and salutations. The problems you're having can stem from several things. To discover what those things might be, we need more information from you. The required information can be found at https://retropie.org.uk/forum/topic/3/read-this-first.
Right up front, I'll say that you must have the correct ROM version of 'Marvel vs. Capcom 2' for the version of MAME that you're using. Assuming that you're using lr-mame2003, which uses the 0.78 MAME ROM set, you'll need to acquire the 'Marvel vs. Capcom 2' ROM from that numbered set. More information can be found here.