MIL relates to the fact that the yellow/orange engine light on the dash is/was illuminated, normally referred to as your Check Engine Light. Does your scan tool display any other codes other than “MIL”.
It can occur that something like a misfire will set a code and the CEL and even when you fix the condition that set the code, like you fixed the number 1 misfire, the CEL and the code that set it, won’t reset, even when cleared by your scan tool, until the Monitors in the PCM have some driving conditions met with no further codes being thrown. That is, you may have to drive it so the PCM resets the permanent code.
Just a wild guess. I have no idea what effect the fuel cleaner and catalyst cleaner might have on a hard #1 misfire.