Just got some time to look at the floor rules, and you’re correct. This seems like it is covered here:
Looking at Extra Cards—Warning
A player looks at a card without being instructed to by a rule, game effect, or ability; a player is instructed to look at a card, but looks at more cards than instructed; or a player resolves an effect that requires a choice between looking at a card and another effect, and the player resolves both choices. Looking at Extra Cards can occur in any game zone, including but not limited to R&D, HQ, the Stack, the Grip, and in play. If a player looks at multiple extra cards in a single action, this penalty is applied only once. If a player puts a card into HQ or their Grip, this is Game Error —Drawing Extra Cards.
Shuffle the extra seen cards with all other unknown cards in that card’s zone until sufficiently randomized. Ice should be replaced in the location it was previously. Be careful to first set aside any known cards from earlier effects, such as Precognition, Test Run, or a run on R&D. After the unknown cards have been shuffled, return all known cards in the appropriate order.
If it is impossible to return the game state to a legal state and it is a premier-level tournament, the penalty should be upgraded to a game loss. For example, if the Runner completes a successful run on HQ and accesses two cards instead of one. There was no legal method for the Runner to access two cards, and so the game state has become illegal.
(p. 8-9, 2016 Floor Rules, emphasis mine)
It’s unfortunate that you got a game loss when the infraction and resolution were so clearly spelled out in the Floor Rules. It’s clear to me from the information you gave that this was not impossible game state to resolve, so the game loss upgrade does not seem warranted.
I guess for the future (at competitive or premier events), it’s good to ask the judge if they can show you in the floor rules what they based the ruling on.