Dear Nati2208,
The results of featurecounts does not show you the mapping statistics it shows you the counting done by feature count. That is to say, You have 50% of the reads that assign to at least two or more features in your annotation file, e.g., two or more transcripts of your gene, or two or more exons because they map to exon-intron boundaries.
I hope I could answer your questions.
Best wishes,
Florian