VEP output SIFT_score unclear
The dbNSFP plugin from VEP accesses tables of data for each variant from dbNSFP and pulls out the values. dbNSFP provide their SIFT scores in that format: a score for every transcript affected by the variant, all on one line. The lookup is just for the variant, not for the variant/transcript combo, so they provide scores for all variant/transcript combos. You can also get a column that gives you a list of the transcripts or proteins (Ensembl_transcriptid or Ensembl_proteinid) in order so you know which score goes with which transcript.

A better way to get SIFT scores with VEP is to get them directly from VEP, rather than using dbNSFP. This will get the SIFT score that goes with the transcript on the line with the relevant transcript.