Translation:Alligators and crocodiles are different.
Can "malsimila" be translated as "different"? Different can be not-similar, also can be "similar but not same". Different only equals to malsama, doesn't it?
Should it accept "alligators and crocodiles are not the same"?
Different means not the same, and the construction, with mal and not, is parallel.
Perhaps, but if you accept that translation, it might be confusing for people. Understanding "mal-" as "not -" is a fairly common beginner mistake, so I think we should err on the side of strict here.