As discussed here, nonstandard columns in the file/dataframe passed to LocalOccurrenceData and LocalOccurrenceDataFrame are not removed, causing problems down the line.
In that example, Background fills that column with NAs, and then removes them with an na.omit() call (that's overzealous and will be another issue).
These two functions should strip any unwanted columns and warn the user that they were seen and removed.