In some occasion the funding fee might go negatives. You can check the funding fee history data and analyze it yourself. If you think that is only temporary, you can keep running the bot. But if you think the funding fee negatives will run for several days or even weeks, you might want to stop the bot and find the other opportunity.
Historically, the average funding fee in a year is always positive, but you can analyze it to know the better condition of the market.