I had a similar experience when finishing my router table.
I called Dad and he basically told me what EarlS said above. I sent him a photo and he said "oh, looks like you've got some Tiger striping action-looks good!"
Well, it was my first foray into Watco, and when my Dad told me that, I didn't necessarily agree with his assessment. I decided to put on an additional 8 coats of Watco (Logic: it will even out with more coats; Narrator: it didn't, only more contrast).
Looking back at the photos, it was actually fine. Do I like it now with 9 coats? Yes. Would I have liked it with one coat? Also yes-I was a beginner, and thought it was unappealing at first.
All that being said … there is an easy way to prevent it.
Grab yourself some wood conditioner (e.g., Varathane) and:
1. Ignore the directions (which are written in a way to make you fail, think it was your fault, and go buy another can)
2. Apply it, wipe it off after 15 minutes, let it dry for 24 hours
You'll never have those dark spots from Watco ever again.
NOTE: Watco doesn't do that to all woods. Pine, Walnut, Oak, ... anything with big fat pores or varied pores.
The "conditioner" is just a wash coat of lacquer that, when dry, prevents the Watco from going down too deep, so you get a nice shallow coat of Watco.
However, I should warn you that this technique gives you a very very uniform finish. So uniform that I actually tend to find the results to be bland and boring. Though, sometimes that's what the project (or customer) calls for, I-for myself-have grown to love the varied stripes and patches that occur in wood naturally.
Yeah, on occasion, I'll bust out the varathane when I have become really attached to the way a wood looks pre-oil, and just want to preserve whatever pattern is in there without disturbing it too much.
As for just going poly after a straight sand … without the BLO component of Watco, you're not going to get the chatoyancy we all love. Though, to be honest, Walnut doesn't have much to offer in that department.