Ahhhh, the number of holes is the issue, too much material is trying to gather for it to be done very efficiently.
You should give a try at doing 6 holes in each pent and 8 in each hex (the two extra, of course, being the ones that connect the hexes) that is the 'standard' method for making bags.
Dude, from the picture, it looks like you are stitching 6 holes. 6 holes = 3 full stitches. It's more a matter of you having too much fabric to gather and the pent/hex ratios are off. Your hexes look huge...
From what I can see, you may need to align your panels better. It seems inconsistent which may also be a reason why your gather is inconsistent. You want your hexes lined up to your pents in exactly the same place one after the other. You may want to try a shorter hex edge length. Shave off however many fractions of inches you feel like shaving off and experiment. I only know metric.
Also, you may want to stitch less deep into the panels as you currently have been. It would mean less fabric to bunch up.
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It seems to me that your short length of the hex is far too long, which in turn makes your overall hex far too large. I think that a 2:1 ratio for long hex length:short hex length would serve you better. In fact the short hex length could be even shorter compared to the long hex length than a 2:1 ratio.
Maybe you are also stitching the hole that goes through the hexes too far into the panel of the hex. as in, you are leaving too much fabric left on your long hex length at this hole so it creates an even longer stitched short hex length than you originally intended it to be.