So there are a couple of things that may be happening here. Firstly, these cookies are made with brown sugar, so they will be darker than conventional chocolate chip cookies and may start to brown more deeply than you're used to. This can make you think they are done early. Once you've removed the pretzel cookies from the oven, also be sure to allow these to cool on the pan for about 5 minutes. This will help them to stay nice, soft and chewy, but will also help the base of the cookie to firm up to make them easier to move across to a cooling rack. If trying to move them immediately from the pan when fresh from the oven, they will be too soft and may fall apart.