The 3-1 loss left the Royal Blues in fifth place and meant they have picked up just five points from their last seven matches.
Their title hopes look all but over and they face a fight on their hands to qualify for the Champions League next season.
"We are ruining our good start to the season," Howedes said. "It's absolutely terrible.
"Things are going a little askew."
Questions have started to be asked too about the future of coach Huub Stevens, whose contract expires in the summer.
"We've got to win our last league game of the year and also get through in the cup, and then we will see where we are and how we can evaluate things," said the club's director of sport Horst Heldt, who before the game told Sky television that Stevens "is still our first choice".
Stevens said his side had "committed too many mistakes, it's as simple as that," but he is still struggling to find an answer for their dip in form.
Stuttgart coach Bruno Labbadia claimed his side who had "forced Schalke into making mistakes".
"We then just took advantage of them clinically," he added, celebrating a victory just 43 hours after his side went down 1-0 to Molde in the Europa League.
"This was a great victory for us."