According to this site, alligators/crocodiles mean hidden dangers because they are situated underwater and hard to see. They can also mean deceit, because they trick you into thinking they are not there.
I find this rather eerie, because now in my adult life I am hyper aware of what I think other people are thinking.
So, why do humans associate feelings and problems with animals? Here is my theory:
Instincts are ridiculous.
Feelings are associated with animals the same way feelings are associate with colors. This all happens on the instinctual and (you guessed it) subconscious level.
Yes, dear reader. It must mean something. The subconscious rarely does things without a purpose. The only thing I can really compare it to is "fate". You may not understand why something has happened to you, but there is a purpose. Or so we tell ourselves to try to make our lives seem less useless. Same thing with the subconscious. It chooses things that the conscious may not comprehend, but there is a purpose.
Remember, this does not mean that we are interpreting these animals-that-are-connected-to-feelings correctly. But what the hell, worth a shot right? And we all know analyzing dreams is some fun shit.