It’s possible that you’re overtraining. If it goes away in a few hours, that normally means you’re fine. Only if it stays around for a long while should you worry.
Occasional swelling of the flesh is normal. Just make sure to watch it, and make sure it subsides. Swelling isn’t necessarily a sign of damage, but sometimes a sign of growth…so don’t quit just because you’re puffing up a bit…just keep being watchful of yourself.
Something I would recommend is doing your stretches before your jelqs (and after your warm-up, obviously). Stretches are better as warm-ups than as end-of-routine exercizes…if you want, you can do both…but I would recommend doing them mostly at the beginning.
Also, stretching might be puffing out your glans simply because you’re doing it at the end of your routine. My cock used to do that all the time, get puffy and weird looking, kinda like how your hands ‘prune up’ when you’ve been swimming for hours or something. That was solved by doing stretches at the beginning, and doing the most hard of exercizes, the most erect ones where the glans is filled with the most blood, near the end of my workout. Perhaps I am wrong, but I believe it is best to put the most intense exercizes near the end, especially ones dealing with high erection/high bloodflow states…it really helps your penis keep the most blood in it for as long as possible, and that helps it grow a lot more than being drained of blood quickly, which is what often happens when you do stretches (because you have to go fairly limp to stretch properly).
Aside from all of this, make sure you’re eating right and drinking plenty of water. Those two things are highly important if you really want to get serious about PE and have it work for you. These two things will also help you recover faster, grow bigger more quickly, and basically maximize your potential all around.
Also, I would exercize at least a little bit every day, or at least every other day. Exercize helps immensely with bloodflow and IMO helps make growth in PE come faster, as well as in greater amounts. That’s not to say you’ll get 2 more inches in a year with exercize, and 2 less without, but exercize definitely impacts it.
Keep up with PE man, be healthy, and stay safe. =)