Hi Belle,
Before calling a microflow show a popup page, in that you can get input from the user and you can call the microflow from there itself.
According to this answer some time ago, it is not possible to pause microflows and wait for user input: https://forum.mendix.com/link/ideas/541
Did this change since then?
For anyone interested in a similar problem – the errors were related to the hybrid phone app homepage pathway not being configured for a role that needed a different homepage!