Don't worry too terribly much about how much CO2 is produced. As long as you burn the same type of candles and use a new one every time, you'll wind up with a lower degree of variabiliy. Also, do two or three experiments and average your findings--it will eliminate possible outliers.
When running this experiment using water, you need to keep in mind the fact that water has a vapor pressure, too, which is NOT insignificantly small. You need to measure the temperature of the water, because the warmer it is, the higher the vapor pressure of the water. My guess is that the temperature in the greenhouse (and thus probably the water) was significantly higher than the parking lot.
In addition, make sure that you are careful to keep the inverted cylinder at the same height from the surface of the water each time. Either sink the mouth to the bottom, or try and keep it just below the surface of the water by affixing it somehow to the container. Although it shouldn't make too much difference, fill the container to the same level with water from the same source each time to eliminate more variables.
When measuring the level of the cylinder, someone else mentioned the cooling of the gasses inside the cylinder. Because of this, you need to measure the level of the water inside the cylinder at the same time after the candle goes out each time. Keep in mind that in a windy parking lot heat is dissapated faster than in a hot still greenhouse. Take a reading at say, 5 seconds after the flame goes out. Make sure your eye is reading from the same level each time and that you're reading the meniscus of the water, not some random part of the water level each time.
In addition, you will have to monitor barometric pressure as well; signifacant atmospheric pressure changes may have an effect both on water vapor pressure and the amount of air you're trapping in your cylinder. This will be a minor contributor, as the atmospheric pressure won't contribute as much as some of these other factors. If you want to check it out, run three replicates at the same place on two or three different days to help eliminate random error.
I did an experiment with butane similar to this one time, and it was a huge pain to get all these factors nailed down--you could change the level of water inside the cylinder by a huge amount just by the depth of it being inconstant. It is theoretically easy, and easy to get some crude answers from, but the difference of oxygen you're looking for is going to be small and may be within the error limits of the experiment.