Bubbles in a syphon tube are likely to be CO2. A beer has considerable CO2 dissolved in it at the time of bottling. When it gets disturbed the CO2 is released. You just don't want to get bubbles or foam in the bottles since this could be caused by the stream of beer mixing air in to it.
If the beer warms at any time before bottling then it will release CO2. Cool it again and it may absorb oxygen from the spce above the brew in your FV. So try to keep the temperature stable.
If the beer warms at any time before bottling then it will release CO2. Cool it again and it may absorb oxygen from the spce above the brew in your FV. So try to keep the temperature stable.