The electrochromic colouration and electrochemical behaviour of sputtered thin films of tungsten oxide (WO3) in a lithium-containing electrolyte have been investigated. We found the behaviour to be extremely sensitive to the deposition conditions. In particular, we have produced WO3 thin films over a wide range of sputtering conditions, and found that in some cases, large amounts of lithium can be inserted irreversibly with no change of colouration. It is found that material showing this effect is predominantly produced by sputtering from a tungsten metal target. Different experiments have been carried out in order to isolate the mechanism responsible for this irreversible intercalation, and the indications are that a single phase of LixWO3 is not formed as is usually expected, but instead we most probably see a chemical reaction of lithium with interstitial oxygen to form a two-phase compound. Our findings may have implications for the manufacture of tungsten oxide thin films for electrochromic windows.