I could suggest carbon nanostructure formation. Despite of temperature, maybe, in ethanol as solvent, it is possible to obtain. I don't want to guess carbon dots due to its current topic of my research work. If I were you, I would illuminate it with UV-light (380 nm). Then, if fluorescence occurs, I think, it will be intresting to investigate its activity via spectrophotometry
I would suggest buying a brand new APTMS first and then changing the functionalization protocol. I prefer doing functionalization of MCM-41 using anhydrous toluene (no need of strict drying; take normal toluene, put some freshly dried molecular sieves, seal it well and keep overnight before using it) at 100 °C (under N2/Ar flow) and this has never happened to me. It should stay as white powder. After the synthesis wash it very thoroughly with H2O-EtOH-H2O. This should solve the problem.
In my experience if some metal is getting coordinated with the functionalized silica, its color may change even at very low impurity level. So wash all your glassware and stir bar with freshly made aqua-regia.