The air in your home is nothing like the air outside. It's naturally still. It's dry. It's enclosed. These factors all present some issues you need to deal with when it comes to your bonsai trees.
Plants are a lot like kids- they don't like their living conditions changed. Sure you can take them to the beach for a day. But let mom colour her hair and the 5 year old will not be amused. Trees are much the same.
Outside your trees experienced moving air and inside - not so much. So what? In still air, fungus, molds and mildew can all thrive, so you need to keep an eye on your trees. Inside about the only breeze you'll get are from hot and cold air vents and that air- pushed by your HVAC system tends to be bone dry and damaging to your trees.
When your trees have spent the summer outside a few bugs are almost inevitable. But outside there are natural predators and importantly, there are lots of other places and plants that aphids and fungus gnats and whitefly can torment. If you bring these new buddies inside with you they are cut off from their predators and they have now been confined to a much smaller space and one only filled with your plants.
The rule is to be vigilant when you bring your trees inside. Inspect carefully for aphids, scale, mealybugs, whitefly and fungus gnats. Mealy bugs, scale and aphids can pretty much be dealt with using physical intervention techniques. Q-Tips dipped in insectical soap are a great tool for removing mealy bugs and scale (Had a great story from a customer who turned some grade 7 boys loose on a heavily infested plant, armed with Q-tips. Happy kids- No more bugs.
You can wash aphids off smaller plants ( might have to do it a few times). At the first sign of fungus gnats use yellow sticky traps to catch the adults before they lay more eggs and a drench made of 50:50 water and 3% hydrogen peroxide will take out the larvae. Again, it might take a few hits.
If you see whitefly on a plant- DO NOT bring it indoors - at the very least don't bring it anywhere near any other plants. Whitefly is about the hardest insect I've found to get rid of.
About the biggest challenge with indoor air is evident by late February or March. It is dry. Killer dry. Junipers kept indoors are super susceptible in early spring when the combination of dry air and strengthening sunlight will kill trees. And spider mites love dry air. ( Wash them off and then put the tree into a large plastic bag to super boost the local humidity) I'm not a fan of pesticides (especially in the house) so that colours my suggestions.
Finally, and no surprise, the indoor air affects how you water. Whether is the lack of moving air- or HVAC air getting pushed at your trees, or just the lack of needed humidity requireing some extra interventions ( local humidifier, spraying, pebble trays) that might affect the amount of moisture getting into the soil. The slowed winter growth means less water will be taken up by the roots so you actually can be dealing with dry foliage and water logged roots at the same time.
But never fear- spring is coming