A first-half double from Lewis Moore saw Hearts win the friendly at Rangers Training Centre, but Thomson feels it is more beneficial for the players to be put in difficult situations.
Speaking to RangersTV after the match he said: “I thought the way we started we lacked a wee bit of personality and I thought they imposed more on us than we did on them.
“At times we found it quite difficult to get out. To be fair, Hearts were a good team and they put us under a lot of pressure and they probably schooled us a wee bit in the first-half.
“I think in the second-half we looked a wee bit more of a threat on the counter attack-but overall it was a difficult afternoon.
“We are happy for them to make mistakes, they are young football players and they are going to make mistakes.
“The bit that I find difficult to accept is if they go hiding from the ball - you need to have big personality, a big character and strong mentality.
“That was probably the most disappointing part for me in the first-half but I certainly thought that they put their foot on the ball more in the second-half and looked more of a threat.
“I thought Dapo looked more of a threat in the second-half and our front boys started to run and show more energy so it gave us a bit more of a foothold in the game in the second-half.”
With Scotland international Christophe Berra and the experienced Zdenek Zlamal featuring for the visitors, Thomson said it provided another different challenge for the players.
He continued: “It makes it harder. Christophe is an experienced player with many many caps for Scotland and he has played in the Premier League down in England so he has real good experience but that's what we want.
“I'll never bother about results, I say to them all the time at this club you need to win but if we come up against older teams and they put us under the cosh and it's difficult that's what we want.
“We want to see the players stress and struggle, we've got no time to watch them pop it around and look like Brazil it makes no difference to me. I want to see them have their nose just above the water.
“It is another learning curve for us. At half-time Michael Beale gave us a bit of detail on out of possession. We were a bit more compact and a bit harder to play through in the second-half but we are still learning all the time.
“Our team is always changing and we are never having a settled group so it is a real big challenge for Brian and I to try and implement all the principles of the first-team but I am enjoying it and hopefully the boys are.”