Nicky Forster bagged the only goal for the Seagulls as the Hatters stayed up by a point after being handed a 10-point penalty for entering administration.
Ward said: "The players haven't been paid this month but hopefully they will be early next week.
"Looking at the season overall, we got ourselves into a great position in December, but then had to move players on and, as a result, put kids into the team."
Stockport captain Michael Raynes felt the young team did themselves proud in the final game and said: "The players have given 100% whether they have been paid or not.
"They would have learnt a lot through the experience. It could have been a great year for us. We will never know what we could have achieved and next season it may be a case of seeing how the young squad develops."