If what your talking about is the shapes are not closing , where the blade cut the path but did not close that path. Im not sure about what cut software you use, but when this happened with me I ended up having to use and exacto knife to finish the small cuts so that I would be able to weed the design without cussing to the vinyl gods. I found that when I enabled the "Overcut' Feature this fixed the problem and I was able to weed with ease and all my shapes were cut completly, This was after I adjusted speed, blade exposure length, etc. It seems that Overcut bring the cut just a tad more than what the software is reading from the file.
In Flexi, this Option is in 'Cut/Plot' Screen and under the 'Advanced' Tab. you can adjust the overcut length, for me 0.100in worked.
Good luck.