You intrigued me with this so I dug out the Greek text and discovered that you are absolutely right about this. Let's take a look, shall we...
Matthew 21:7 (translated from the Greek), "They brought the donkey and the colt, and upon them they put the cloaks and Jesus sat on them."
Now, the first "them" (they placed their cloaks on them) refers to the donkey and the colt. When talking about mixed genders (the donkey is female and the colt is male according to the Greek text) the masculine term is always used. In Greek a pronoun must always match its referent in case, number, and gender. The word for "them" used here is masculine because it is referring to both the donkey and the colt.
The second "them" refers to the cloaks. We know this because the word for "cloaks" is "imatia" which is a neuter word. The pronoun used for the second "them" is also neuter. It also must refer to the closest referent in the sentence, otherwise another word in Greek would have been used. It therefore MUST refer to the cloaks. It cannot refer to the animals at all.
Bottom line, Jesus didn't sit upon two animals, He sat upon a number of cloaks, placed upon the animals. It cannot be deduced at all that Jesus sat upon more than one animal. Therefore, this passage agrees perfectly with the other Gospel accounts.