My problem with creationist thinking is closed-mindedness with which they approach the subjects of alternative creation beliefs or evolution. Before they even engage in a debate they "know" that they are right and everyone else is wrong. Before they even know what the other side is saying, they have made up their minds that it is wrong.
This way of thinking is then projected onto science and scientists by creationists who just can't grasp the concept that science is prepared to change it's ideas when new evidence is unearthed.
Any scientific evidence which is presented as contrary to a creationist stance is handwaved away as wrong, bad science, evolutionist dogma etc, they don't take the time to find out just what the evidence comprises, how it was obtained and the implications of it.
My final and biggest problem with creationist thinking is the sheer arrogance displayed when a creationist with a pathetic understanding of science tells scientists that their science is flawed.