A report from the Hants Journal over at NovaNewsNow.com says that the brown longhorn spruce beetle (Tetropium fuscum) has actually been around in Canada almost a decade longer than entomologists originally thought. It turns out that specimens of the Eurasian invader were collected in 1990 but were misidentified as a native beetle in the same genus. It was not until 1999, when another infestation was discovered in Halifax, Nova Scotia, that an entomologist went back to the 1990 samples and the mistake was discovered. That means the beetle had quite an opportunity to spread unheeded. There are now over a dozen sites in Nova Scotia where the beetle can be found, leading to quarantines of wood products and threatening the local logging industry. Unfortunately, Canada doesn't seem much closer than they were in the late 1990s to developing an effective treatment to protect its forests, so for now the Forest Service is continuing with its "containment by cutting" method of management. That incensed groups like Friends of Point Pleasant Park, who were quite active a few years ago when this story originally broke - they were convinced that the government was overreacting.
Update: In the comments, Monique brings up another example of an invasive species hiding by misidentification, a parasitic plant species in Texas (Orobanche ramosa). The point here is not to belittle the identification work that biologists are doing - I know it is a gargantuan task to keep track of the various characters that define plant species, and especially insect species! It is just interesting to consider whether focusing more resources towards rigorous sampling and cataloging of flora and fauna might benefit us in the long run if it enabled us to successfully prevent invasive species from becoming established.
The other case I can think of off the top of my head is the invasive aquatic plant Hydrilla that was found in Connecticut in 1989 but misidentified as another invasive, Egeria densa. The error was not discovered until 1996. Got more examples? Post them below!
Update 2: Thanks to Chris for pointing out various inaccuracies in the article (see comments on this post). This might have been a recycled news story but it is the first time the brown longhorn spruce beetle made it onto the ISW's radar!