Despite signing a new deal 24 hours before kickoff, defender Schlotterbeck was jeered throughout the 1-0 defeat to Bayer Leverkusen.
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Upsetting fans was news that the new deal includes an escape clause worth €50-60m should offers come in for Schlotterbeck during and after this summer's World Cup.
The clause can only be triggered by a select number of clubs, including Real Madrid and Bayern Munich.
Former Germany midfielder Khedira said on DAZN: "If you renew your contract and leave three months later, nobody likes it, especially in such an emotional environment as Dortmund.
"That's why they're outraged."