I suspect the fiberglass cloth is more the culprit here than the film or bag over it.
After all, FG is stiff yarns snaking around each other, and doesn't really like to bend in a tight radius at a sharp corner. And it is bending at a radius, unless all the fibers are broken. So some bridging, be it at millimeter scale or smaller, is going to occur.
The problem is twofold, first, bridging creates a stress concentration, second, it is visible.
If there is enough resin in the groove, the resin will form a fillet under the glass, solving both problems.
Whether you are wetting glass on a separate table or on the board, you can do a lot to avoid this
problem by loading the groove of the chamfered deck layer with resin before laying the cloth over it.
Vacuum will draw the excess resin through the PF or peelply and the bridging problem should "disappear."
The 3M 77 if you aren't familiar with it is a type of sprayed contact cement.
Spray the core with it (very lightly, sort of like spraypaint overspray) right before you lay the glass on. It will hold the FG down in contact with the core and help some against bridging.
The 77 is just another trick, mainly useful if you are laying dry cloth onto the core. It keeps the cloth aligned properly by tacking it down, and you can press the cloth into any grooves or chamfers and it will stick until the resin takes hold. It is not visible or harmful in the finished piece.
With 77 you may still have the tiny amount of bridging due to the stiffness of the glass, so you will have to make sure enough resin gets pushed under/through the cloth to fill the space.
If you just round over all grooves to a bit more radius, the glass may lay right against the core.
But looking back at your pictures, the most important factor may be you vac setup.
It looks like you are pulling air down the length of the board to a single vac fitting, with just a patch of breather under it to form an air passage. This can make the glass creep and undo all the above steps to avoid bridging. It is advantageous in normal vac bagging to make the air travel a short distance, and do so symmetrically to avoid disturbing the laminate. More breather and a central vac fitting should suffice, as in the picture, at left:
bridging.png [ 26.8 KIB | Viewed 499 times ]
At right is what I suspect happened to your board.
If you are aiming for a perfect-out-of-the-bag finish and want to keep the fitting off the board surface so it doesn't leave a mark, you can make vac channels down the sides of the board with rolled breather or spiral tubing instead and keep the vac fitting(s) off the board.
Your work in general looks very neat, you will be able to produce great looking boards when you get this dialed in.
Edit: final thought and sorry for such long answers, if the pics above of the board under vacuum (with wine glass) are not right after starting, but a while after the bag has been on, it may just be that you are a little lean on resin and need to use just a bit more to fill these little voids. I'd expect to see the resin spreading over the PF a bit more than it is in the pictures. Trust the vacuum to pull out the excess.