There are a number of possibilities:
1) Did you calibrate your thermometer? And are you absolutely sure there were no breaks in the mercury column? (assuming a mercury thermometer, of course)
2) Was the bulb of your thermometer entirely immersed in the vapor that you were attempting to measure a temperature for? A change in position of 5mm is enough to make the reading completely unreliable.
3) Was the toluene collected pure? You can measure the boiling point of the collected product - if the boiling point of the product is also 90°C, then your setup was correct and your toluene is impure. If the boiling point of your product is 110°C, then either the thermometer position or the thermometer itself is wrong.