I like collecting badges in pairs, when possible. I recently noticed that two of my questions had view counts in the mid-900s, so I decided to go for a pair of Popular Questions. After getting them some attention they both passed 1,000. However, I only got one badge.
One of the questions, Simple Lisp Program Causing Computer To Hang, seems to have been deleted in the interval between passing 1,000 and the badge-awarding-script running. If the script had been scheduled slightly differently, I think the badge would have been awarded.
If the cause is just this coincidence of timing, rather than by-design, this seems like a bug.