Rovers came close to earning a point in Devon until Conor Grant converted from 12 yards in added time after Kieran Agard went down in the penalty area.
Wellens felt that the Plymouth player dived to earn that foul as Doncaster remained rooted to the bottom of the table.
Earlier in the contest, the visitors had gone ahead through Jordy Hiwula-Mayifuila’s strike before Plymouth equalised with their first penalty of the day, converted by Luke Jephcott.
“Is it a penalty? It probably is a penalty, but week-in, week-out, you will see people getting to the by-line, and pulling a cross back, the defender going into them, and it will not be given,” he said.
“The second one is not a penalty, Pontus says he hasn’t touched him, I watched it back – the lad’s dived.
“That was a different class performance. When we went 1-0 up, we changed a little bit, and we went a little too passive.
“We created chances, we could have had a lot of goals today. We’ve come here today and we were better than them, in our shape, the way that we played.
“That gives me a lot of satisfaction. My only negative would be that we got a bit panicky when we were 1-0 up.”
Doncaster have won just one league game this campaign and face another long trip on Tuesday evening as they head to Ipswich Town, who have also only managed one win in League One.
Plymouth Argyle: Cooper; Wilson, Scarr, Galloway (Gillesphey 74); Houghton, Edwards, Camara, Broom, Grant; Jephcott (Agard 88), Hardie (Garrick 80). Unused substitutes: Burton, Randell, Law, Shirley.
Doncaster Rovers: Dahlberg; Knoyle, Williams, Anderson, Rowe; Close, Galbraith, Smith (Barlow 78); Hiwula, Dodoo, Cukur (Vilca 72). Unused substitutes: Jones, Olowu, Bostock, Seaman, Gardner.
Referee: T Kettle (Rutland)