Top of the server means the highest league level teams on your server.

CL draw is, in part, a numbers game so if there are not enough teams of same level teams (multiples of 32) someone gets pulled up into it. Can happen at any level but most likely towards the top. Same can happen in leagues.

Adding bot teams seems sensible but can bring additional problems unless they are specifically to fill a CL gap then disappear completely. Not so easy for leagues unless it was managed. Ofc "beaten by a NordGen Bot! Rigged!" might appear here more.

Another option would be just to give a bye or walkovers if not too many gaps - with appropriate rewards ofc re cash etc to compensate.