Tracking movement vs intercepting communication is a very different thing. In general, any attempt to spy on an ally is going to get a lot of egg on your face if it comes out, and if it's using tools your ally helped finance and/etc, you can bet it's going to get complicated.

In this instance, Israel needs the US, Pegasus was Israel's technical gorilla in the spy world, and it got used on the US by someone they sold it to. This level of fallout given that is not unexpected; Israel cares more about maintaining ties with the US than they do about a given tool, company, or to enable Ugandan spying operations.