Looks like total number of parts and sum of them differs on bricklink I've recently purchased the 42063 BMW R 1200 GS Adventure.  It was assembled and looked complete.  I took it apart and calculated total number of parts.  It was around 550. Then on link above I've read total is above 600. With about 10 extra still about 40 less. I rechecked individually starting with rare ones than actually went through all list.  

Discovered maybe 3 small ones missing,  but again maybe I was  not attentive,  also discovered that some parts could be taken apart which I missed initially.  With extra it was about 570 finally.  

Still about 30 less than expected total. My guess is that maybe total includes all stickers separately even when they are listed as 1?  Why else can be such discrepancy? Can somebody proficient with bricklink API sum up the list to check against total?
Brickset says 602 elements, brickset takes its data from Lego Customer Services.

Bricklink says 603 elements, bricklink count includes a stickersheet while brickset does not. To get the bricklink total, select "Part out" on the catalog page, it will suggest to add 603 pieces to a "wanted list".

Adding the number of elements in the back of the manual I get also 602 elements.
Going through the instructions and adding all element counts I get 598, this certainly does not include any spare parts, so about 4 spare parts seems right.

Conclusion, your set is lacking elements or you miscounted.
I think easiest would be to group by element and count and see if those counts match the brickset or bricklink list or the back of the manual inventory.
Plus side will be you have everything sorted and you'll know exactly what pieces are missing.