If the message is colored as spam in Mail and shows as Predicted: Spam in the log, it sounds like SpamSieve is encountering an error when trying to move the message. SpamSieve 3.0.1, now in public beta, includes some changes that may help with this.
A red log entry means that it took an abnormally long time to process that message. This could indicate something unusual about the message that tripped up SpamSieve or simply that your Mac was overloaded with other tasks at the time.
SpamSieve 3.0 will add a gray flag (3.0.1 uses orange instead) if the Mail extension encounters an error processing the message. Please use the Save Diagnostic Report command in the Help menu and send me the report file, as described here, and I’ll investigate further.
High memory load on your Mac could slow down SpamSieve’s processing, though I wouldn’t expect it to cause errors unless it’s so bogged down that things start timing out.