Dealing with the machine not cutting the design you may have correctly, could be a variety of things.
Most common, is the machine is not properly calibrated or tighten correctly (in specific areas).
To calibrate the machine, go to the settings(alt-6) page, and click the set steps per unit(right above the reset button). You will receive a tab which asks to select the a axis, once selected it will ask how much you plan on moving. Here you will enter a value of inches/mm's. The machine will move what it thinks is the correct length and might be dead on or might be off, we recommend doing this about 2-3 times per axis, and in long distances. (ex: for the BF you may do 2-4Ft on y-axis and 5-8Ft on the x-axis)
Make sure the v-groove bearings are tight, on the y-axis plate and z-axis, as well as the v-groove bearings on the gantry legs. (test: try moving them with your finger, if tighten correctly they will not move)
Also having the chain too loose will not move the machine enough to create your design, the chain should have about a 1" - 1"-1/2" of slack in the middle of the table when the gantry is in either of the far ends of the table. (larger machines will have a bit more slack).
Trying to run the machine faster then the bit can cut, or running with a old endmill/router bit.
This is a rare occurrence but is seen, having the correct endmill, feedrate, and RPM will have a great impact on your cut. They all work together in one complete conjunction, if one is off they will all be working incorrectly.
Each endmill will have its manufactured specifications.