So weird bug, whether i use a controller or keyboard, when i go into the character select screen, after a second or 2 will automatically select a character without me even pressing a confirm button. Anyone else had this glitch? cheers.

Yeah this happens, but it's a simple fix:

in install location locate dosboxMortalKombat3.conf
open in notepad
in CPU section change cycles from auto to 40000
save

Should be fine when you launch the game now.

EDIT:
Also if you're in the install folder you might as well open up dosboxMortalKombat3_single.conf and on the penultimate line change:

mk3

to

mk3 666 1000000

and save. Now when you launch the game you can select Smoke as well as Montaro and Shao Kahn (though 2P only for those two).

cycles=fixed 20000 without any quotes works more or less reasonable

Thanks for these tips guys, just picked MK1+2+3 up on sale.