Contrary to what Google says, you can't depend on WMT links data to disavow links. Here is a chronological list of one of my recent experiences with WMT links data -
1. Site slapped with manual penalty - 745 domains/32k+ links
2. Links from about 100+ domains removed for a total of 30k links (One particular site had sitewide from 25k plus pages). After 3 weekks, WMT started showing 180 domains/10,000 links. Many sites from where links were removed still showing and some not. Sitewide site had gone.
3. More links removed. After another 2-3 weeks WMT data refreshes, and this time 630 domains/30k links. Sitewide site has again made a come back, from where links were removed over 2 months back.
Imagine if I had started link removal process when the data had showed only 180 domains.