Tom Blomqvist, Josh Pierson and Oliver Jarvis had moved into the class lead after a storming stint in the wet from Blomqvist when the Briton briefly went into the gravel.
Upon approaching the Porsche Curves, he found he had no brakes and made contact with the barriers which triggered the in-car medical light.
Once cleared after undergoing medical checks, Blomqvist returned to the cockpit as the repaired car finished eighth in class, although not before the left-front wheel parted company with Jarvis.
"This looks like it’s something in the gravel trap that’s damaged the brake line, it’s not a piece of gravel," Dean told Autosport when asked about the #23 entry's first incident.
"Who knows, there was so much debris out there, there could have been a car buried in there! It’s difficult to tell at that time of night because the replays don’t show it.
"There’s some damage on it, it’s an unusual thing, but unusual things happen at Le Mans."
Dean said it was not yet known if the problem was linked to Blomqvist's visit to the gravel, but suspects this was the case.
"We need to really properly investigate it," he said. "You fix the car here and you get back on with the race rather than start to have an inquisition.
"You look at the series of events, of ‘he’s gone off through the gravel in one corner, the next corner he’s got no brakes’, you suspect they’re linked. It’s unusual for a trip through the gravel trap to have that effect."
Explaining the crash, Blomqvist said: "I was trying to slow the car down, just couldn't stop the car, had to look for the escape road and then eventually the car spun out and hit the barrier.
"It's a huge shame because we were in such a good position. I don't know, the amount of times I've been through the gravel in my lifetime and not once have I had a brake failure from it.
"The chances of that happening are so [small] - just luck wasn't on our side."
United believes the left-front wheel later detached because of damage to the retaining pegs when the wheelnut stripped during a pitstop.
"They put another one on and then four laps into the stint the wheel has come loose," said Dean.
"Again we have to do proper investigations but we suspect that when the wheel went on and stripped it, it’s damaged the retaining pegs and damaged the thread.
"We put another hub on, didn’t have a repeat of it. But those sort of things put you out of the race at Le Mans don’t they?"
He added: "We’d have had the pace to make a race of it at the front and just we sort of got into the lead, it started to unfold.
"It makes it even more painful to watch when you know you’ve got the pace.
"I think we’ve got some really good stint averages and all the drivers looked quick.
"But we’re not the only disappointed people here today. In that first six hours, a lot of garage doors were shut [due to retirements]."
The sister #22 United car lost time when Le Mans rookie Freddie Lubin lost control on the Mulsanne Straight passing GTE Am traffic on the bumpy apron and crashed into Mikkel Pedersen's Proton Porsche, which later retired due to the damage incurred.
A 26-minute stop for repairs and a three-minute stop-go penalty meant Lubin, Filipe Albuquerque and Phil Hanson were out of contention and finished 11th.
"It was a mistake, he knows it, but he’s in pretty good company here with some drivers making some mistakes," said Dean.
"We put him out in a position where we’re telling him that we’re in a race-winning position and giving him the hurry-up not to lose any unnecessary pace.
"You’ve got to walk the drivers through these things, so we can always look at ourselves to say ‘could we also do something different’ in guiding him through. We all take a bit of responsibility."
