I'm seeing three options:
1) PM asked Queen to prorogue without stating a reason.
2) PM asked Queen to prorogue for non-Brexity reason.
3) PM asked Queen to prorogue for Brexity reason.
If in the middle of a time sensitive crisis the PM asked the Queen to shut down Parliament for an unprecedented 5 weeks without giving a substantive reason why, and she said, "sure," without asking a follow up question... that seems like a problem.
So either the PM lied to the Sovereign or one accepts the politically convenient suspension of Parliament just happened to be called upon for other, non-Brexit reasons, at the exact moment the Prime Minister needed it.
As with Option 1, it seems systemically problematic if a PM with a governing majority in the -40s walked into the Palace and received royal assent for "This legislature keeps legislating and it's bumming me out, can you suspend it?"