As the title says. I put fusion engines in all my trains on aquilo and none can take fuel unless I get in. This would be a minor inconvenience if not for the fuel being deleted when I get out.

Please give specific steps that can reproduce the problem. I tried using a locomotive with a fusion engine and I could not reproduce the problem. The locomotive can accept fuel, and the fuel does not change when entering and exiting a locomotive.

Your second sentence describes the behavior of a locomotive that doesn't have a controller. However, fuel is not destroyed when exiting these locomotives, as you can observe by checking your inventory after exiting a locomotive. Partly consumed fuel is also not destroyed, as you can observe upon re-entering the locomotive.