In Steins;Gate, aren't the time machine crash and screaming mutually exclusive?
If I get your question correctly, then the answer is NO. Those do not contradict each other because


   The events you described above (first half of episode 1) happens in the beta worldline. In the beta world line the time machine is complete - hence there was no coordinate error and the machine did not crash. The time machine only crashed on the alpha worldline.


I hope that answers your question.