Looks like you didn't clean the glue on the joints well. That's why the stain isn't taking there.
Discussion
That's superglue btw. It's always a pain to see it before a layer of stain. Now I'll sand it off, stain again, then a couple of polies.
I'll post an update when it's done.
Nice! Yeah, I think if you wipe it with paint thinner in the future during the glue up you can avoid that. Nice build!