This happens because the rules say something like "in prime season check in or check out has to be on a Friday Saturday or Sunday"
so for example if you want a Wed to Wed vacation. It has to be two reservations Wed Thurs and Friday (check out Saturday) followed by another reservation ...Sat, Sun, Mon and Tues (check out Wed)
It also happens based on availability. The Wyndham "mother ship" stores the reservations as weeks that start on Fridays, Saturdays, or Sundays. Depending upon the resort, the percentage can be different. Whether a particular stay will require a split depends upon what's already been taken and what that would leave.
For simplicity's sake, let's say there are 3 2BR units in a resort, one each of Fri, Sat, and Sun. Let's say you want to book Friday-Monday. That will ordinarily take the first 3 days of the Fri-Fri reservation. If you book far in advance, you can probably get that; but within 90 days, a lot of budget-minded travelers vie for the Sunday-Friday reservations available from Fri-Fri weeks, since weekend nights are usually about double a weekday. If someone has grabbed the Sun-Fri, then only Fri and Sat remains.
So in our example, you want to stay Fri, Sat, and Sun night. Someone has booked the Sat-Saturday week, someone else has booked Sun-Fri from the Fri week. You can only get your reservations from the Fri week plus a portion of the Sun week, and only if it doesn't create an "island" night (single night stay) which is only allowed within 10 or 15 days of check-in (not sure which). So sometimes, even though a resort has availability for the unit type you want, for the dates you want, you still can't book it, or can only book it by booking an extra night.
It can be frustrating to be sure.