I've seen this with wetlay / vac bag before.  You can really poke the cloth into the corners before applying vacuum but you still get this problem.  For me it was down to the release film.  The film I had was a certain perforation rate which didn't allow enough resin through into the breather.  The resin flows around the cloth without going through the film and you end up with resin collecting in the features like this.  The bubbles you have are probably this problem combined with not degassing your resin sufficiently.  Try switching to a higher perforation level on your film or try lowering the resin loading on your lay up.