First of all the whole mucoid plaque thing is a myth. I addressed this several times:

 http://curezone.com/forums/fm.asp?i=1509584#i

http://curezone.com/forums/fm.asp?i=1510653#i

It is hard to say what you are passing without a description. Most likely it is either blood from the damage to the intestinal wall that it can cause, especially if there is inflammation. Or it could be darken stool from the spirulina if it is not being absorbed properly.