MvC3's combo system is really lenient with regards to inputs, but there are a lot of moving parts and general techniques that you have to know in order to actually make them work, so I can see how someone who isn't super familiar with fighting games (at least on a competitive level) might struggle with that initial hurdle.
I don't really know much about Injustice's combo system, but if it's like MK9, then it probably just has some weird timing mechanics that you need to figure out in order to make them work. Again, just little things that if you don't know how to look for will give you a lot of grief.
For MvC3, I would just start doing really basic (in other words: bad) combos just to get a feel for how moves cancel into the other. Then you should work on things like wavedashing, tiger knee inputs, triangle jumping (for certain character like Magneto), and other input tricks that make certain combos and setups possible. Also, knowing the exact timing of your assists through practice is essential too. Everything after that is just getting the right feel for the timing and flow of it.
One thing to note though is that MvC3's meta game is very unique among current fighting games. Matches essentially play out like high intensity games of chicken, where one player looks for that first good hit and goes for the kill combo as soon as they get it (sometimes they can't, but usually they can). After that, it's a mental exercise between the two players of what setup the victor of that particular "character match" will go for to trap the incoming character. The cancelling system makes concepts such as "safe" or "unsafe" moves virtually nonexistent, and you won't punish people for them but try to extend the neutral game in order to get another opportunity at landing a hit.
Basically, MvC3's a weird fighting game all around, lol
