You need to wait until the bot's energy is completely gone before you can recharge them.  If the bot shows a symbol showing a small amount of energy and you then click on it, you will pick the bot up.  If the bot shows a symbol showing no energy and you then click on it, it will be recharged. 

You can also train bots to recharge other bots.  If you train a Crude Bot or a Basic Bot to recharge other bots, you will need more than one bot so that the recharging bot will also get recharged.  I suggest that you train a Steam Bot to recharge the other bots instead.

I have set my Steam Bots so that before they do their task (such as Recharge Worker Bots shown below) they will take a log from storage and stow it in their inventory, meaning they recharge themselves.  If their inventory is full, the log is still in their hands and so it will be added back to Log Storage.  If their inventory is not full, the "Add to Log Storage" is skipped.