David Ngog scored an outstanding opening goal before Tangerines forward Tom Barkhuizen's controversial equaliser just before half-time.
Celebrations were cut short as the assistant referee had his flag up for interference in the build-up. However, after consultation with referee Simon Hooper, the goal stood, to the disgust of the Wanderers players.
But Ngog then worked hard to set up Jermaine Beckford for the winner on the counter in the second half.
Thompson said: "We've got to take the positives out of the game.
"We created a lot of chances and their keepers made a lot of saves so it's disappointing that we didn't win the game when we played like that. On another day I think we come through.
"We looked like we had energy and even in the defeats we've had we've shown what we can do.
"We just need that little bit of quality to finish that off which I think that we do have in the team."
Meanwhile, despite the Trotters' complaints, Thompson believed the Tangerines' goal should have been given.
He added: "It's one of those grey areas but they couldn't disallowed that because it was a fantastic strike.
"I'd have been disappointed if we didn't get it but likewise we were disappointed that we conceded that goal just after half-time."
Thompson also admitted Blackpool were looking to recruit imminently, adding: "There's a lot of things ongoing at the moment and hopefully it will be a busy week for us."
- Sports & Recreation
- Tom Barkhuizen