The rocket weighs quite a bit less at the end, having used most of its fuel, so only two engines are needed to land. The engines cannot be throttled down more than ~50% (as all rocket engines), so a third one would add too much thrust.

Falcon 9 does the same, relighting 3 engines (out of 9 total) for the boostback burn, 3 for the entry burn and then just 1 for landing.

For that flight the engines are even too powerful for the ascent (it wasn't fully fueled, I think) and as soon as they couldn't throttle any lower, an engine was turned off instead.

Thanks for the explanation! it this also the reason why Raptor is (relatively compared to like F-1) small and BFR uses so many of them?

That, and for redundancy. I've heard it's designed so that even if a significant number of engines malfunction, others can be used to compensate.