The USA national team captain signed for 'Gers from French club Saint-Etienne last Wednesday before taking the field for the Europa League play-off first leg in Slovenia on Thursday but Maribor believe that he should not have played.
Maribor spokesman Zelkjo Latin made the point that Bocanegra may not have been eligible as he was not allowed to play in the Scottish Premier League on the weekend.
"How can he have the right to play in the European competition on the Thursday but didn't have clearance to play in Scotland three days later?
"We are now awaiting a decision from UEFA. We're mentally preparing for the match as if it is 2-1," he said.
But Rangers have denied any wrongdoing, saying they are surprised by the allegations.
"We are extremely surprised by the complaint of NK Maribor," read a statement on the club's official website.
"As confirmed by the SFA, Carlos Bocanegra was deemed eligible to play at a domestic level within the UEFA deadline in accordance with the requirements of the UEFA regulations.
"We have at all times acted with due regard to the requirements of the UEFA Europa League regulations and we are confident that the complaint by NK Maribor will be rejected by UEFA."