Factual error: As the X-Men land in Cairo, scenes reveal the destruction Magneto is wreaking around the world, where it is simultaneously daylight in New York, Sydney and Cairo - it is possible for it to be daylight in two of these locations at once, but not all three. (01:46:00)
Factual error: When Apocalypse touches the television in Cairo and says he is "Learning", the next shot shows the rooftops with many smallish satellite dishes in view. This is set in the early eighties when satellite dishes for TV were much larger.
Factual error: When Stryker's chopper with the mutants on board flies over the lake it enters a tunnel that barely clears the rotors. As any student pilot could tell you, this would lead to an immediate crash as the downwash from the rotors struck the bottom and sides of the rounded tunnel and reduced lift to zero.
Answer: As shown in Days of Future past, Trask was able to identify Magneto and Mystique, as well as their mutant powers. Trask could have found Charles Xavier at any given time, or Stryker possibly researched him. Stryker did work for Trask after all.