Faultfinding, whether a design that's not working as expected or a failure in previously working equipment, is along the lines of a "Differential diagnosis", to steal a medical term.
What parts of the circuit/system/machine could be related to the fault?
What parts could not be related?
Of the parts that could be related, which could be causative and which are side effects?
Pin it down as far as possible, then compare what it it doing to the components/parts involved, to try and figure out what type of fault or failure could cause the effects you are seeing.
Use or add test points; with an FPGA, you can use spare outputs or temporarily swap outputs from an area that is unaffected, so you can see what is actually happening on a scope or logic analyser.
If you are working with other people, talk it over with them and explain the system and fault in as much detail as you can. If on your own, still explain it out loud as if you were trying to explain to someone else, down to the finest detail.
It forces your brain to re-process what you know and can often lead to new answers to a problem.
And don't rely purely on simulations - they are useful but not always perfect. As another user on here has in their signature:
“
In theory, theory and practice are the same. In practice, they are not.”