There are a couple of possible causes. One is simply the quite substantial increase in your cycling compared to previous years. A bit of wear & tear is to be expected. It could be exacerbated by technique; if you're a low cadence "grinder" you would stress your joints more than if you're a spinner, and that stress is going to invrease through the extra distance.
Alternatively it could be a cleat position problem, causing your knees to twist and mistrack slightly. Here's a quick test: sit on a table with your legs hanging freely. Observe the angle your feet naturally point. Your cleats should be positioned so your feet are at that angle on the bike. If they're not, then you'll get knee misalignment problems. Hope this is a good start.