Beer gets mixed up when siphoning into container just before bottling
When preparing to bottle a cerveza style beer (from a kit), I moved my beer into the primary fermenter so that I could mix in some sugary water before bottling to make my beer bubbly. The beer had been especially cloudy since it was in the primary fermenter but had cleared significantly. As I siphoned my beer I noticed clumps rising to the surface, falling down, and disintegrating into the beer. Overall the beer is getting super cloudy again. I did mange to eliminate some sediment at the bottom but I feel that it is not up to my regular standards. Should I go ahead and bottle or let it settle once again before bottling?
Also I wonder what could cause this. I believe I had left the beer in the secondary fermenter for a full 3 weeks, often I procrastinate/ am too busy to go ahead and i leave it longer but I understand 3 weeks in the secondary should be sufficient. Am I right on that? Is this something to do with Cervezas?