In my experience, it could be either.
After fermenting, even though beer is not 'fizzy', it will have CO2 dissolved in it. When it is siphoned out of your fermenter, the reduced pressure in the siphon tube will cause
some CO2 to come out of solution, which will rise to the top of your siphon tube. This
could be the bubbles that you see. If that's the case, then there is nothing to worry about.
On the other hand, any crack in your siphon tube or racking cane, or any join in your siphon that is not fully sealed can be a place where the reduced pressure in your siphon tube can suck in air (which contains oxygen) and this
could be the bubbles that you see. If this is the case, then this will slightly oxygenate your beer. This isn't the end of the world, but isn't desirable. There are threads on oxygenation you can read-up on.
In short, I don't know, but you have more information now
(my siphon tube is opaque, otherwise I'd tell you whether it's normal to see bubbles or not)