If you have chosen the QvSAPOLAPConnector.dll or QvSAPDSOConnector.dll from the drop down list in the Data tab in the Script Editor, there will be no mismatch check between SAP Transport and connector version.
However, the rest of the connectors will do the mismatch check.
Which connector are you using when receiving the error message? Please attach the log file for the connector. (Log file location: C:\ProgramData\QlikTech\Custom Data\QvSAPConnector\Log)