I would make the case that many of them did understand the threat of a two party system arising. George Washington (unless I am misremembering, our only Independent president) spoke at length about the dangers of political parties during his farewell address.

I have already intimated to you the danger of parties in the State, with particular reference to the founding of them on geographical discriminations. Let me now take a more comprehensive view, and warn you in the most solemn manner against the baneful effects of the spirit of party generally.

...

The alternate domination of one faction over another, sharpened by the spirit of revenge, natural to party dissension, which in different ages and countries has perpetrated the most horrid enormities, is itself a frightful despotism. But this leads at length to a more formal and permanent despotism. The disorders and miseries which result gradually incline the minds of men to seek security and repose in the absolute power of an individual; and sooner or later the chief of some prevailing faction, more able or more fortunate than his competitors, turns this disposition to the purposes of his own elevation, on the ruins of public liberty.

Washington understood the dangers posed by political parties and, if you read the address in full, it becomes clear how correct many of his suppositions were. One thing that is important to remember when looking at this issue is that political parties are not expressly dealt with in the Constitution. It was something that Madison, Hamilton, Washington, and others warned against as detrimental to a healthy republic, but it was never expressly forbidden (or even addressed in the Constitution). It is also worth pointing out that most of these men eventually became members of political parties themselves.

So, yes, many of the Founders did anticipate the rise of a party system (or at the very least feared the rise of such as system). They did not, however, see fit to take action on it in the Constitution. Why this is, is probably a question better left to an expert in the area., hopefully one of whom can chime in. My knowledge most comes from Political Science and Constitutional Law rather than a strictly historical knowledge of the time period.

A couple more sources: Federalist Paper No. 9 and Federalist Paper No. 10 also both cover political parties.