The reason this happens I think is that MakeMKV rips what gets outputted if you select "Play All" which TV shows tend to offer as an option on the DVD menus for each disc. You should be able to deselect this output of the program before the ripping the selections you make when the disc is initially read by Make MKV

If you can't and the only option is to rip the entirety of the "Play all" selection, then you can either use a lightweight video editor like Movavi to partition the giant video file into episodes. Or you can do what i would prefer if i had this problem and use a program like DvdFab (paid) or DVD Decryptor (free) to turn your DVDs into ISO files which preserves the DVD menus and everything like that when you play them in VLC or w/e

For example, when I have ripped my professional wrestling DVDs, i rip them into ISOs because i don't want one giant video file of all of the wrestling matches on the DVD, i still want to be able to select the match individually so i can pick and choose more quickly which match i can watch. But that is just one example, and i don't watch professional wrestling that much anymore (just something i did for a few months for nostalgia kicks last year)