The books make it seem like if you just staple B+C strips together at the forms everything will turn out fine. But- you need to ensure that you have an actual glue joint with contact along the length of the strip, not just at the forms. To achieve this you need to do just like you do if you're gluing up anything else- add pressure until you get squeeze out along the entire joint. I stripped cove up, so between strips i used little pieces of 1/4" dowel to protect the edges of the strips and added clamping pressure with blue masking tape, usually 1 or 2 between each form, but if there are difficult curves I used as many as necessary. Even beveled strips need clamping pressure between forms- don't think that method is magic either. Glues are not, as a rule, structural. They only work properly when the two pieces being glued are in contact with each other. Reduce the contact, reduce glue strength. If you have poor glue joints in a kayak it's less noticeable because the strips get covered with fiberglass, but think about if you built a piece of furniture with poor glue joints. A chair with bad glue joints might look cool, it is sure to fail, probably in short order. So, while the books make it seem like stapling at the forms will magically give you a glue joint, I find it better to ensure I have a good glue joint, just like when I build furniture.

Now- as for your current problem. If you could post a photo it would help, but my inclination is to just glass it and forget about it. Epoxy will seep into your voids and make small lines, maybe a little bit darker than your stock. These stand out a lot less than bright lines from trying to fill all of the gaps with putty, because you tried to guess the final color of your wood after its been wet out with epoxy and didn't quite guess it right.

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