It makes complete sense for them to refuse in this case. The documents didn't line up. But without an explanation being provided for the discrepancy, they had no option but to refuse.
A simple statement from the company explaining what happened would have prevented the refusal. But without that - how is UKVI to know that everything is above board?
Well, I'm not a lawyer or a border control officer. And, from lurking on this forum for the past few days, I appreciate you have a great deal of expertise in these things, KFDancer.

It's just that if I had a letter from the employee confirming a sponsor's employment and salary, plus six payslips and six months' bank statements showing the flow of money between the two parties in excess of the minimum requirement, then, yes, I'd be satisfied that the financial requirement had been met.
Two months not being an exact match wouldn't throw anything into doubt if the amounts were otherwise clear of the minimum. And, if it did, I'd confirm with HRMC. At the very least, I'd reach out to the applicant to clarify the discrepency. As you indicate, a statement from the employer could have dealt with this very quickly.
But, just rejecting it out of hand?
It just seems a bit mean-spirited to me.

Tim