Sounds like they just renewed in advance. What is "Renewable in advance by" set to? If you've set a bonus time and they renew within that bonus time it renews them for next year giving them the remaining months of the current year for free. Specifically the "Bonus time before first period start (for calendar-based durations)" and "Bonus time when reactivating expired subscriptions" parameters control this. Did you change the plan duration after users have already subscribed as that can also mess up calculations? Example as follows.

Regular Validity duration: This calendar year
Start date of calendar year: 01-01
Bonus time before first period start (for calendar-based durations): 3 months
Bonus time when reactivating expired subscriptions: 3 months
Renewable in advance by: 1 year

Using the above if I subscribed right now I'd have the following.

subscription_date: 2017-12-12 15:44:00
expiry_date: 2019-01-01 04:59:59

The 3 month bonus time gives me the rest of 2017 for free and subscribes me for 2018 expiring on the first of 2019.

Be sure "Manual renewal extends expiration date as follows" is set to "Renewal starts at expiration date or at payment date - whichever happens last (allows free gap)". Sounds like you're not allowing renewals to start from payment date and are instead only extending their expiration date in which case it's working as intended.