The main reason for this is that a lot of "top-up" votes went to lots of small parties, none of which got enough to win a seat. For example, in Central Scotland, 12% of the votes went to minor parties. Also, the proportionality is within each of a number of relatively small regions, rather than across the whole of Scotland.
Then, the d'Hondt system for distributing seats proportionally tends to favour larger parties: it keeps the ratio between actual seats and ideal seats as close to 1 as possible, rather than keeping the absolute magnitude of the difference close to 0. In Central Scotland, the last seat was distributed to the SNP, leaving them with 56% of the seats compared to 46% of the votes, a ratio of 1.21. If it had gone to Labour, it would have had 44% of the seats compared to 35% of the votes, but a ratio of 1.24.