The defender picked up a calf problem in training during the international break, but Lambert feels the 29-year-old was rushed back into action too soon following a thigh issue.
Senderos' absence, which could last up to a month, leaves Villa desperately short at the back, with Nathan Baker (knee) and Ron Vlaar (calf) already sidelined.
"The one I'm not happy about at all is Philippe," said Lambert. "He is the one which has annoyed me the most.
"He went away with his national team and, if you look at his record, he has only played six minutes, against West Ham, for a month.
"He goes away with Switzerland and ends up pulling his calf in a training exercise.
"It's mismanagement from the FA in Switzerland. They should have been in dialogue and seen his record in the first place and that he didn't play for a month.
"It's OK for them to go away and think 'we have only lost a centre-half' but we have lost a centre-half for a month again who has been a vital part of the team.
"We still have options but in Philippe's case it should have been avoided. He was totally fine when he came on in that little cameo role against West Ham."
Aston Villa host Southampton in the Premier League on Monday.
