I am trying to imagine your exact process, so bare with me. Don't move the plants first, and if you do, do it gently. And how do you get the siphon going? Best thing I've found, take the tube of the vac in the corner, pump it up and down in the same spot, so you are only disturbing that one timy spot, until it gets sucking. then slowly move it around, digging it down in the gravel, let it suck up the gravel and the organic waste, then lift it slowly and the gravel should fall out with the organics going up the tube. move over an inch or so and dig it in again, repeat. don't just dig up the substrate (Gravel is substrate by the way). You might not get to clean all the gravel this way each time, that's ok. do another water change in a few days. And do another area.
short answer, don't just tear up the substrate, pick a section, put it in gently, and get everything out of that area.
Also, you have only one beta? If there is that much on the bottom, either feed less, or feed more slowly. Sounds like you've got a lot of detritus on the bottom.
