you don't hit any hotkeys manually on your keyboard at all when using MCE (at least that's the idea).
There are two modes when using MCE with PF3:
Mode 1: "You have ATC". As far as I am aware that is the default setting of MCE. It means that the user does not talk to ATC but to his first officer (=MCE).
For example you say "request ATC clearance", MCE says something like "okay" and you hear MCE say "Frankfurt delivery, Lufthansa 123 requesting clearance IFR to Heathrow" and MCE will send the hotkey 0 which PF3 detects. You hear PF3 giving the clearance, you hear MCE read back the clearance and MCE sends the roger-hotkey.
Mode 2: "I have ATC". With this setting you talk to ATC directly. You press your PTT-button and say "Frankfurt delivery, Lufthansa 123 requesting clearance IFR to Heathrow". MCE sends hotkey 0. PF3 give the clearance, you read it back while pressing the PTT button and MCE sends the roger-hotkey.
You can switch between these two modes any time by saying "I have ATC" or "You have ATC" (there are other phrases as well like "my radios" etc.). There is no options menu to make this setting.
You can also use a kind of hybrid mode. While in "I have ATC"-mode you say "request clearance" without pressing the PTT-button. MCE will comply as in mode 1, but not automatically read back and send the roger key. You can read back yourself while pressing the PTT-button and MCE will send the roger-key or you can say "reply to ATC" and MCE will do so and then send the roger-key.
You can of course still manually press the hotkeys yourself on the keyboard if everything else fails.
So maybe the user was in "I have ATC"-mode or it was a glitch in MCE. MCE is still being adapted to the new phraseology of PF3. In particular the phraseology around the clearances given on ground have changed a bit and at first MCE did not correctly recognize the transmissions because the keywords changed (e.g. the new "report ready to taxi"). There were some patches by MCE recently and I think it is still in ongoing development. So the user has to make sure to be on the latest version of MCE.