No, there's a specific Negative Quality that allows players to get points for having that particular condition
at game start. Don't confuse 'has a Negative Quality' for 'can only take it at game start', or 'cannot be imposed in-game'. Let's look at the specific condition, huh?
TLE-x
Vector: Special
Speed: See Description
Penetration: 0
Power: 5
Nature: Degenerative neural condition
Effect: Stun Damage, Disorientation, Paralysis
Technically not a pathogen, temporal lobe epilepsy with complications is a chronic and degenerative neurological disorder resulting from extended neurological and metabolic stress (typically the result of excessive cyberware implantation, especially move-by-wire implants) and as such follows much the same rules. If a character develops TLE-x, she does not manifest symptoms immediately; instead, she becomes subject to acute epileptic seizures in stressful situations. When in appropriately stressful circumstances, the gamemaster may call the TLE-x victim to make a Body + Willpower (3) Test. If the test fails, the character suffers a seizure, and the “disease” effects above kick in.
Initial onset may be resisted by a pharmaceutical cocktail known as AEXD (see Biomedicals below), but after onset TLE-x can only be treated via corrective gene therapy (p. 88) or brain surgery (threshold of 20 and a DV of 7P) — though in both cases it may return if the cause is not removed.
Underlining/bolding in the text is mine.
This is a condition that MBW users may develop - and from the sound of it ('initial onset may be resisted'), something that they will eventually but inevitably develop. No, MBW doesn't say anything about it; I call that an error on the part of the writer. However, presuming the GM is
aware of this condition and that move-by-wire is a primary (but not solitary) cause, the GM should a) warn the player that this is very possible, b) inform the player about the aforementioned AEXD (500 nuyen a week), and then c) if the player doesn't take that drug cocktail regularly, should start noting this in his GM plot journal. When the failure to take the drugs hits a threshold, perhaps 100/level of MBW, then the character develops TLE-x at the GM's whim.
Complaining that this is a random enforcement of a Negative Quality is, well, lack of research; I took two minutes and discovered the base information here, which is found in the description of the aforementioned Negative Quality. Complaining that a GM is enforcing negative qualities (ones which are 'simply' accepting a future possibility as being present) on a whim or for his own amusement is like complaining that you didn't take a Negative Quality of 'Bullet-Riddled' and that the GM is imposing it on you when corporate security is working on filling you full of lead.
TLE-x (or epilepsy, really) is part of the baseline 'Move-By-Wire' inasmuch as a) it's a condition (like 'Blind' or 'Incompetent') that you can take at Game Start, and b) it's a condition that is like any other disease that the GM feels like exposing you to - except that in this case, you-the-player get to choose whether or not to expose yourself by taking high levels of reaction enhancers and/or taking the drugs that help suppress the condition. Negative Qualities are not the only way for Bad Things to happen to you; they're just one way for you to decide that they're ALREADY happening to you, and you might as well get points out of it.
Do your research, JustADude. It'll help your game satisfaction.