Five strangers trapped. One of them is not what they seem.
You note that the second sentence is “jarring”, and you claim “the writer was obviously using a singular they”. Compare ShreevatsaR's suggestion, “... Only four of them are what they seem”, where they, like them, clearly is plural. If you think of them and they as plural in ShreevatsaR's version, you may find it easier (and a little less jarring) to think of them and they as plural in the original version. (That is, in both cases “what they seem” refers to how the group seems, not the one.) In short, it is not obvious that the writer was using a singular they.
For a better version, I think ShreevatsaR's suggestion is good, but I think leaving out “Only” and changing “what” to “who” improves the dramatic impact:
Five strangers trapped. Four of them are who they seem.