Not too long ago my Webmaster Tools backlinks count decreased from more than 500 links to less than 100. Did anyone have the same issue?
Nope I never have faced any issue. Maybe you lose your backlinks. Just work on creating quality and permanent backlinks.
check your backlinks on backlinkwatch.com, GWT does not always give the correct report and provide the outdated report so it would be better to use the third party tool for this.