My current understanding makes it entirely plausible to run out of cards in the probe droid deck.
31 (Probe Cards) - 5 (Starting Systems) - 1 (Rebel Base) = 25 In Deck
At a rate of 2 cards a turn, the probe droid deck will be empty at the refresh phase of turn 13 this makes it unlikely but possible. Adding in "Gather Intel" to the mix makes this a plausible occurrence though uncommon. If the probe deck is empty would you just no longer be able to draw from it (Rapid Mobilization)? Is there an event that involves recreating or putting cards back into the probe droid deck (Ignoring that one rebel card that puts 4 back into the deck)?