Are you using the TFL site? if so, you can select (bottom right) which modes of transport to include/exclude. Limiting it to tube, overland and DLR may gie you a better idea of the options.
Buses may be suggested of the journey is shorter or because stops are closer to your planned destination (this is particularly likely if you are navigating to a postcode).
They tend to do engineering works at weekends - I think Cannon Street station is closed every weekend at present, for instance, and they're ding some work on the Northern line which means it's often partly closed at weekends, but there's nothing major that week.