The Spurs manager had become aware that United were courting the England international and then took exception to an embrace between Jose Mourinho and Dier following United's 1-0 Premier League win, which he interpreted as an unofficial approach.
Pochettino and Dier then held a four-hour meeting to discuss the exchange between the player and Mourinho, with the ex-Sporting Lisbon youngster explaining that the embrace was not linked to any intention to move to Old Trafford.
"The manager's point of view was [the friendliness with Mourinho] was disrespectful to him," the 23-year-old told The Sunday Times. "[The dialogue] was more him getting that message across than me getting my message across.
"I grew up in Portugal. Portuguese people are very proud and it's a small country. It doesn't have the economic power of a country such as England, so people like Mourinho, [Cristiano] Ronaldo, they're extremely proud of it. Growing up there I was within all that, you know?
"I didn't want to be disrespectful to anyone. I completely understand where the manager was coming from but I believe I was stuck in the middle of something I couldn't really affect."
The saga escalated when Pochettino sensed that Dier's form had been affected by the interest from United – his advisers were keen on the move – and the former Everton youngster admits he did not live up to expectations in the wake of the speculation.
"It probably took six months — January, February — for my football to get better and a lot was my fault, my attitude, and that didn't have anything to do with Man United," he added.
"I just didn't have the commitment, the work rate I should have had, and communication with the manager about the whole situation wasn't good. But never did Man United . . . never did it turn my head. I was never thinking, 'I need to go.'
"There was so much to it and everything accumulated and was like a big snowball and that's where it ended up exploding. If we'd communicated better we'd have avoided that. I learnt so much from the whole experience and I think the manager did as well."
Dier would later be linked with a £60m (€68m) move to United last summer but Tottenham held firm, as Mourinho successfully pursued Nemanja Matic from Chelsea to supplement his midfield. But the incident left Pochettino fuming.
"Maybe it is a common Mourinho tactic, but he put Eric in a compromising position," he wrote in the new book Brave New World: Inside Pochettino's Spurs. "You cannot do that after a defeat.
"'Are you friends with Mourinho?' I asked him. 'No, but I've known him a long time, from my time in Portugal... one of his godsons coached me. He always says hello.'
"I sat down with Eric after lunch on Monday and we chatted for four hours about the whole shebang: his agent, family, confusion. As for the Mourinho incident, 'What could I have done?' Eric asked me. He told me about United's interest since last summer  and I explained the situation to him clearly."