I wonder if these events caused by malfunction or pilot's failure to follow checklist.

Certainly pilot failure. A mechnical issue would be caught by the pilot
99% of the time by the pilot when he noticed a gear unsafe light. There
are some very rare cases of gear not being down but indicating down but
that's not common. Its more likely a busy pilot not noticing. I've
heard tower call out gear up to pilots before. Usualy the pilots are
thankful but sometimes they are irritated.

-Robert