As for sensor temperatures, this should only happen if the individual dark frames have either different values of sensor temperature in their metadata, or no metadata at all. For FITS, our ImageIntegration tool supports the CCD-TEMP header keyword, so if your acquisition software writes different keywords, here is the reason. Typical FITS interoperability problem.
For exposure times, we support the EXPTIME and EXPOSURE keywords, which are used by all acquisition applications as far as I know. Exposure times are added for all integrated frames and the integrated image receives an EXPTIME keyword with the total sum. If this does not happen in your case, then the only reason I can figure out is that there are no valid EXPTIME or EXPOSURE keywords in your frames, which would be weird.
To help you further, if possible, we need a sample of the dark frames you are integrating.