Do you mean that the cells are migrating too much, dead or are they rounded-up? If migrating it is worthwhile to add Rock inhibitor to your culture dishes. Y-27632 at about 1 uM. If your cells are too much rounding up and struggling to settle a coating of e.g. poly-l-lysine or fibronectin could help. If they are dead, your treatment in combination with trypsin could be too severe?
To be able to answer your question, it would be helpful to know more about your cell-type and what treatment you gave to cells for the assay. Two days is not sufficient time to see "colony" (because not enough time for cells to undergo cell divisions to give a colony, assuming that the cells are "clonogenic".
Two days is not sufficient time for the formation of cell colonies as also pointed out by Dr Choubey. For this, you should wait for atleast 7 days, thereafter, stain the cells with crystal violet or giemsa stain for clear visulaization of colonies. Hope this will help.
Dear Herve, as pointed by eminent researchers above, would you mind giving us more details about your cells type and your clonogenic assay conditions. Moreover, 2 days are just not enough to expect a good result.