was this converted from finaplix-h? if so the clear, thick orangeish sediment at the bottom is some of the glues used when making the pellets. if it sits long enough it'll just stick to the sides and bottom of the vial and you don't ahve to worry about it. even if you inject it, it was designed to be implanted, so i wouldn't worry too much about that.
if its a powdery cloudy sediment then you most likely cracked your syringe filter when you were filtering. in this case i definitly WOULD refilter it as the syringe filter is what is used to sterilize the mix and if it were cracked then you very well could have gotten more than just some sediment into the final product.
for $5 i'd rather be safe than sorry.