Most of Kyoto's everyday public etiquette isn't written down anywhere — it's absorbed by watching what everyone around you is doing. Here's the shape of it, so you're not learning entirely by observation.
On trains and buses
Queue in the marked lines on the platform rather than crowding the doors, and let passengers off before boarding. Phones are kept on silent ("manner mode"), and voice calls are generally avoided on trains — stepping into the space between carriages if you genuinely need to take one. Eating on a regular commuter train is generally avoided, though it's normal and expected on long-distance trains like the shinkansen.
Escalators
Kyoto and Osaka, along with the rest of the Kansai region, traditionally stand on the right and walk on the left — the reverse of Tokyo's stand-left convention. It's a genuinely real regional quirk, though increasingly inconsistently followed even by locals; watching what the people ahead of you are doing is the safest guide in the moment.
Rubbish
Public bins are noticeably scarce in Japan relative to many other countries, a legacy partly of past security concerns — the practical result is that you're expected to carry your rubbish with you until you find a bin (often back at a convenience store or train station) or your accommodation. Carrying a small bag for this is genuinely useful.
Smoking
Smoking is increasingly restricted to designated areas rather than allowed freely on the street, with signage marking permitted zones — lighting up outside a designated area, even outdoors, is a common source of unintentional rule-breaking for visitors.
Volume, generally
Public spaces in Kyoto trend quieter than many visitors expect — trains, restaurants and shrines are all spaces where a lower conversational volume is the norm, not a house rule specific to any one venue.