When shaking nonpolar solvent with aqueous sodium carbonate, very tiny water droplets can be formed and these may float in the nonpolar for quite a long time. Put the jar aside for maybe 15 minutes to allow the tiny droplets to settle and stick to the bottom of the jar. After that, the nonpolar can be decanted into a clean and dry jar for freezing.
Even with plain water washes, the micro droplets will interfere with freeze precipitation by freezing into water ice "snow" crystals. These are rather harmless, they will evaporate together with the nonpolar solvent remains.
Another option is to pour the nonpolar through some coffee filters, these will absorb the water droplets. This will only work if there only a tiny bit of water in the nonpolar, it is not a replacement for a separating funnel. It may also cause quite a bit of DMT-laden nonpolar solvent to be left behind in the paper filter, making the extraction less efficient.