It is neither the points, nor the controllers at fault, which are performing as designed: but the limitations of the set track system, which is intended for children to run a train with a controller per track circuit.
The moment you put a crossover across two independently powered track circuits without modifying the points and paying attention to track power wiring, problems of the kind you describe emerge. There's no short cut, you have to understand what to do based on the 'why' of it, and a major help is a good book such as this:
Buy Model Railway Wiring By C.J. Freezer. Available in used condition with free delivery in the UK. ISBN: 9781852601737. ISBN-10: 1852601736
There are now much better options readily available, flexible track systems from the likes of Peco of superior design to deal with connecting track circuits, and DCC control whereby you can drive all the traction from a single controller. Happy New Year!