There are some pretty awesome pattern swatches that come in each Vector Mill Crate. You probably also have a bunch you have created or found along the way in your Illustrator career. I love pattern swatches but sometimes I get frustrated when transforming objects with pattern swatches applied to them. Sometime transforming will mess up the pattern. There is a pretty easy fix.
Transform Tile Patterns Preference
Go Illustrator > Preferences > General and in the Preferences panel, disable the Transform Pattern Tiles option. Now you should be able to transform objects with pattern swatches applied to them without messing up the pattern. If this is not the effect you are going for, you can always switch it back on!