I'm fine with there being an explicit deviation from reality. "Angels and Demons" has one, spending a few paragraphs about how it explicitly broke conservation of energy. I'm fine with that, as it fits with the theological overtones of the book as a whole.
It's everything else that makes no sense whatsoever.
* A single lone researcher getting beam time on the LHC, without anybody knowing what the experiment was doing. I don't care how brilliant a person is, you're not doing experiments at that scale without having it be approved ahead of time.
* Perfect antimatter containment in large quantities. There's going to be some leakage, resulting in detectable gamma rays.
* Portable antimatter containment. Penning traps require large magnetic and electric fields, not exactly conducive to transportation.
* Countdown on a storage device with no safety margin. I can understand having a countdown to the engineered safe period. I cannot understand having the storage device shut off at exactly that time, rather than continuing to use whatever power it has.
* Inability to track wireless cameras. There is a camera pointed at the hidden antimatter containment device, and no attempt is ever made to track the signal from that camera.
* Failure to use binary search. (This is the only one that doesn't occur within the plot's setup, so avoiding giving spoilers.)