That might be aphids - I can see there are black dots on the stems, but can't tell what they are. Looks like the Thyme is desperate for more light and possibly a bigger pot, though obviously I can't see the pot itself - they are hardy outdoors, but it will need hardening off properly before moving out permanently.

I’ve seen no sign of aphids- no sign of anything, except for mottling on the leaves and those minute dots which turn into a brown smear when wiped off. The thyme is certainly potbound, but lives on a south-facing windowsill where it receives plenty of light. I plan to prune everything but the sage down to the ground, and pay close attention to what happens to the regrowth. Thank you for your suggestions.