The Hornets went down 1-0 to the Potters at Vicarage Road over the weekend, with a first-half own goal from keeper Heurelho Gomes separating the two sides.
Prodl was frustrated by the result and says Watford were "unlucky" as he felt the visitors didn't do enough to win the match.
"We had a plan, and I think they played good football, but they weren’t dangerous with the way they played," he told reporters.
"They didn’t create great chances, and scored a set-piece. They had some counter attacks. [Xherdan] Shaqiri had a good game but didn’t manage to create big chances.
"We weren’t able to play our game how we would expect. It was a close game, it was tough, it wasn’t a good game and in the end it’s an unlucky result.
"We’re disappointed, but we have to carry on, step up again and keep focusing on the next game."
He added: "Stoke are a good team, it was an equal game and we lost 1-0 unfortunately.
"We were unlucky, it was a close game again and Stoke have been in the Premier League for 10 years, we were equal to them but I don’t think it’s a big shame to lose against Liverpool or Stoke.
"The way we lost wasn’t that good, but I didn’t see they were that good."