How to paste RSIDs in CADD output
It would be useful if you show us some line of your CADD.bed and Input.vcf and how your desired output should look like.

bedtools is complaining about non positional records in CADD.bed, which means there are lines in this file where the first three columns aren't CHROM, START, END.

I guess you will have some header lines in the beginning that aren't introduced by an #. Just delete them (or add in # to the beginning of the line) and try again.

fin swimmer