The log hours moved with the redesign of the updates area. The new commenting experience was in beta for while but recently became the default for all users.
There are few places you can look to troubleshoot this but I would start by checking the share settings on the issue to make sure the user has at least contribute access to the issue and that log hours is enabled.
From the project level you can view the access rights of the users that get assigned to issues and create defaults access rights for them.