I haven't been rejected yet (fingers crossed) but I can provide another possible issue. In February 2014, I got educational assessments for me and my partner through ICAS. We planned to apply for FSW, but discovered than an LMO would be required, and I knew that it would not be possible to get it for my job as a literary agent. Instead, we waited a few more months and applied through CEC at the end of 2014. The educational assessments we had in our files were not necessary for that application.
Like many others, we got our applications back in February, because the CEC cap had been reached. We immediately signed up for EE and used our educational assessments for points. We got an ITA on March 27 and filed our PR application May 7, the day after we had our medicals.
On June 11, we got a very angry email from ICAS, saying that we had only their "general" assessment, which wouldn't be valid for CIC. They demanded another $145 each to "upgrade" our credentials, and said that even though we did not have to send more documents (our schools had sent documents directly to ICAS the first time) it would take 20 weeks to accomplish.
Of course, we sent the upgrade application and $145 immediately, on the 11th. We also frantically looked around and, discovering that WES could provide results in 20 days, and my school could send the transcripts in 2-3 days, we signed up there as well.
Today, June 16, we got a "request letter" from CIC, saying that ICAS had refused to release our results to them and asking us to call ICAS and ask them to release our results. CIC knew that we had not gotten the "CIC-FSW" package, and advised us that we might have to ask for duplicate reports to be sent to CIC. They did not attach a time period for us to respond.
I called ICAS today to ask if, having paid the upgrade fee, things might move faster since they don't have to analyze any additional documents, but was told to send an email, which I will do tonight.
SO - ANOTHER possible way to run into trouble is if you have an ECA performed before EE, which was done by one of the certified agencies, but not for the FSW program or for EE!