Seen Minimig? Replay? all using various debug tools. Once you got an FPGA wired as Buster you could use it to debug itself and peripherals.
Indeed. Xilinx has Chipscope. Alteras has SignalTap. Open-Source has Sump, Sigrock, OpenVeriFLA, perhaps others. These go inside your FPGA, and may need some on-board memory to buffer what it measures for later analysis, so you don't need a hugely expensive benchtop logic analyzer tool. If something is off-spec, use one of these things to see what is actually happening, and use your engineering imagination to figure out how to deal with that. Something I really wish I had right now is an FPGA board that plugs into a PCI-Express slot and has another PCI-Express slot on top, acting as a man-in-the-middle spy to capture what goes through it for later analysis. Seems that should not be tremendously expensive, yet quite useful.