Even the teeniest/tiniest upward or downward force on where the transmission alignment pins are between the transmission and engine will prevent separation of the two. A sixteenth of an inch of jack height on the transmission can make it a go or no-go separation. I've had it where just the slightest barely perceptible change in jack height made it happen. It's the alignment pins holding it and friction/force on them will cause them to hang up instead of pulling out.
Same thing when bolting the transmission back to the engine. And don't try to pull it together with the bolts if they don't want to pull together, that can strip out the threads in the block. Same process with it... a tiny up or down adjustment will make all the difference.