Registering the on_message event with @bot.event will override the default behavior of the event. This may cause prefix commands to stop working, because they rely on the default on_message event handler.
Instead, use @bot.listen to add a listener. Listeners get added alongside the default on_message handler which allows you to have multiple handlers for the same event. This means prefix commands can still be invoked as usual. Here's an example:
@bot.listen()
async def on_message(message):
... # do stuff here
# Or...
@bot.listen('on_message')
async def message_listener(message):
... # do stuff hereon_message handler with bot.process_commands(). However, this method isn't recommended as it does not allow you to add multiple on_message handlers.
If your prefix commands are still not working, it may be because you haven't enabled the message_content intent. See /tag message_content for more info.