This happened to me as well... I was missing 300+ contacts but not sure which ones until I went to call them or would receive phone calls/texts with no names attached. The missing contacts were completely random. However, it happened after I re-installed and set-up my work e-mail exchange... To fix it, I went to settings, then to "mail, contacts, calendars" then to my e-mail account, then switched contacts from "off" to "on" and all 300+ missing contacts re-appeared. Hope this helps...
Seems my problem was mixing iCloud and local sync'ing - iCloud to iPad and local sync'ing to iPhone since I had data issues with AT&T (surprise!). Once I made contacts iCloud to both and overwrote the iPhone the problems cleared up. Steered in this direction by AppleCare support person, though one of the orneriest support persons I have encountered. Either she hung up on me or we got disconnected and she never called back, but she pointed me in the iCloud vs Sync direction.