"Lewin's tackle was unprofessional and I've spoken to him about it in the dressing room," said Johnson.
"He's a good young player, but he has to learn from that mistake because it was the last thing we needed.
"Again we have let in a last-gasp equaliser and feel like we have lost, rather than drawn. I don't know what more we can do except to keep drilling the players on how to clear their lines.
"At the moment when the stoppage time board goes up it seems to create a siege mentality and we cannot hold onto the ball. It has cost us so many points this season and I'm more than frustrated by it."
Lansbury was stretchered off as a result of Nyatanga's tackle and the midfield player, on-loan from Arsenal, faces a scan in the next couple of days.
Watford manager Malky Mackay said: "It's a nasty ankle injury. But we've already opened talks with Arsenal about extending the lad's stay with us and I don't expect that decision to be affected.
"We have a young side and I'm very proud of the way they kept battling right up until the final whistle.
"City's goalkeeper has pulled off a string of fine saves in the second half and I was starting to think it just wasn't going to be our day.
"But we knew of their tendency to let in late goals so when five minutes of stoppage time was signalled I felt we still had every chance."