The Belgian was pushing for a place in the Hyperpole session ultimately topped by Antonio Fuoco in a Ferrari top three sweep when he rotated the WRT-run M Hybrid V8 on the exit of the fast Piratella left-hander.
Having avoided contact with the wall and got going again, Vanthoor felt the session was red flagged "a bit too early" and wants clarification on the decision that means he will start 13th in the car he shares with Raffaele Marciello and Marco Wittmann.
"It didn’t really give me a chance," Vanthoor told Motorsport.com. "I was still rolling, I didn’t stop the car, I didn’t have any issue. I was just rolling down and trying to go on power again.
"And before I knew it, it was a red flag. For me, it’s a bit of a harsh red flag. It cost us.
"At the end of the day, I ruined a bit my own session with making the mistake. But of course it doesn’t really help when you don’t even have the chance to even get back [on track].
"It’s harsh, but I think we should learn from it, we should look into it why it came so early."
He added: "I’m a bit annoyed that I made the mistake first of all. The lap I was on – it only was half a lap, true, but it felt like a really good lap until that moment. So it’s annoying."
WRT boss Vincent Vosse was equally frustrated by the red flag call, as off-track moments for Matt Campbell's Porsche and Brendon Hartley in Hyperpole were covered by yellow rather than red flags.
Vanthoor had set the second-fastest time in Saturday morning's third practice session, and Vosse said "we would expect him to be yes, in the top 10". His team-mate Rene Rast qualified the sister #20 BMW in seventh.
"Probably they [race control] were surprised that he was able to keep on going," Vosse remarked.
Vanthoor said the expected difficulty of overtaking at Imola will mean "strategy will probably come a lot into place" as the #15 crew seeks to recover and Vosse conceded that the qualifying mishap "will make a difference because here, your track position would be quite important".
But while acknowledging "it will for sure not be easy, it’s not easy to overtake here", Vanthoor expressed optimism that the car will be able to recover.
"We’ve got a good racecar, we’ve got good race pace, so I do think there is a possibility to come back," he predicted.
"It’s a six-hour race, a lot can happen, especially with the GT cars we have to try to overtake. So I do feel quite confident that we will be able to get back quite fast. It will not be easy, but I think for sure it’s possible."
Rast admitted to making "a small mistake in the last corner" that he believes potentially cost him sixth place to Kamui Kobayashi's Toyota GR010 HYBRID Le Mans Hypercar.
But triple DTM champion Rast was encouraged by the progress BMW has made since the first outing for its LMDh car in the WEC in Qatar, where the Bavarian marque languished in 15th and 16th after qualifying.
"We can be very happy with what we have achieved already in the second WEC race, being in the Hyperpole is obviously more than we expected after Qatar," he replied when asked by Motorsport.com whether there was any more potential in the car.
"The goal should be to collect points. Realistically, we can be in the top 10 tomorrow, we have a good pace in the long runs."
Asked whether its car is more suited to Imola than Qatar, Vosse stated: "We’ve been working with BMW, we’ve been working very hard since Qatar on making steps. We were surprised by our situation in Qatar and this looks a little bit more where we have to start."
