There's many ways of measuring porosity, see this review:

Article A Comparison of Micro CT with Other Techniques Used in the C...

If you have limited equipment, instead of the graduated cylinder method, you may get better results using a good analytical balance and using the Archimedes method. You weigh the sample dry, saturated, and submerged in a non-solvent liquid then you can calculate the volume of the open pores from the mass of wet scaffold minus dry and the bulk volume from the mass of the displaced liquid (saturated-submerged). The ratio will give the open porosity. You can calculate the total porosity by comparing the density of your material and the density of your scaffold (dry mass/bulk volume).

Please go through this article were different methods for porosity measurement is given.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826579/

I've never done liquid displacement a method to measure porosity, but I've done a gas displacement method instead. Because I had the same problem as you (small sized scaffolds) I measured 10 replicates at the same time. Maybe that's also a possibility for you?

Article Multimodal pore formation in calcium phosphate cements

Thanks for your recommendations; I used another method like in this journal, but my results were more than 100 %!

For example:

P=(W2-W1)/pV1

Where W1 and W2 indicates the weight of the composites before and after immersing, respectively, and V1 is the volume before immersing, ρ is a constant of the density of n-hexane.

W2 = 0.196 g, W1 = 0.020 g, V1 = 0.235 cm3, p=0.654 ……..

P = 115.032 !!!