Thermometer fluid is separated, defective?
No, it is not defective, just slightly damaged, possibly from shipping. You should call customer service at Cole-Palmer and see if they will replace (or repair) the thermometer.

If not, there are 2 ways to fix it. I haven't tried either one, so I don't know how well they work.

If there is a bulb at the top and the thermometer is low range (under 150°C), then you would heat the thermometer in an upright position until all the bubbles are pushed up into the bulb. 

The other method is to cool the thermometer down until all the liquid is in the bottom bulb. The second method may not work if the liquid freezes before all the liquid has moved into the bulb.