I don't think they are microscopic. Anyhow I have not seen this as a problem...I strain the brew quite well with my funnel. Also when you pour the brew into the injector most of the thick stuff stays on the bottom of the bucket for reuse.
I have used this system for about 2 months now and see no difference with the output of the soaker hose, only in my mater forest
The first 3 weeks I used mostly alfalfa bales in my brew and no chicken manure. Boy did that make a big difference in my plants.