Falcon
My experience is yes, water in the feed or reflux can cause flooding as the result of being a trapped component which will eventually have to burp itself out. Typically the formation of a second liquid phase has a distinct temperature profile the point in the tower where it forms. It will appear that the tower has two modes of operation- i.e. the temp profile will jump to a new temperature and then flatten out for no apparent reason.
This phenomenon may last for a few minutes, or days depending on the cycle. During this period the tower may appear to flood prematurely, and operators often learn to make a move (such as cut reflux or increase heat) to assist the burping action before the tower floods. Later when the water phase disappears the temperature will drop back to normal. This has been my experience on several towers, and in all cases was associated with a second phase.
best wishes,
sshep