If you look at the bass staff, there is one more 16th note than there should be on a 4/4 time signature. Can someone explain this to me? And what is the number of top of the barline?
The three eighth notes (not 16th notes) with the "3" above the beam are a "triplet": three notes in the space of one beat. There are exactly four beats in the measure.
For instructions on how to enter triplets in Sibelius, see the Sibelius manual entry "Tuplets - how to create".