If your CdSe/ZnS quantum dots are aggregating, the most noticeable change should be an increase in light scattering. The wavelengths that are scattered should depend on the sizes of the aggregates formed. It's hard to say, however, whether this is the cause of the dips in transmittance you're observing.
In this case it is better to speak in terms of absorbance (absorption) spectra, not transmittance. In case of core QDs (CdSe for example) the aggregation will result in more diffused band gap optical transition. It may look in transmittance (T) as an increase of T from the short-wavelength side and a decrease from long-wavelength side.
In case of core/shell QDs, such changes will be observed only for the optical transition belonging to shell (ZnS, 450 nm region), but not to core (CdSe, 600 nm region). So, in principle it may look as an appearance of dips in T spectrum in the region of ZnS band gap optical transition.
In order to be sure, you may also have to do some DLS mesaurements , and for sure you will see if your QD have been aggregated or not . Moreover, you can let the solution relax on the bench and after some hour you will notice that your particles will percipitate . Finally you can use PTFE filter ,as if they have been aggregated the particles will stay on the filter , otherwise you are going to obtain solution with the same optical density (using this methods you have to take under considaration that if the particles have been aggregated will stay in the filter and will be really hard to take them back).
I have checked it after keeping it relaxed for some time but no sign of precipitation is observed. The dip that I am getting is at around 800nm and i have coated the CdSe/ZnS (in toulene) on glass substrate by spin coating. And size of my quantum dots are around 8nm. I am not sure from where the dip is coming, so I was just guessing if aggregation has some role to play in it. And from the answers from you and others it looks like it is coming from something else.
The absorbance is also visible at around 610nm(which is quite ok according to previous literatures) but in comparison to absorption, the dip that I am getting at higher wavelength is much more visible or you can say much more deeper. But still, to be sure I will measure the absorption spectra and also the luminescence spectra for my sample.
defects (mainly surface defects) usually make additional peaks in fluorescence spectra and in absorbtion spectra as well. It comes usually at lower energies.
If you use spin coating, you can check the size of the nanocrystals by using AFM (if your coating methods is good, your particles do not aggregate). Using DLS you measure the hydrodinamic size of particle and it is bigger than the size of particle, but you will see if your particles are aggromerated because the aggromerated size is more than two times larger than the individual particle.
Aggregated particle also able to form suspension with low precipitation speed. If the size of aggregated particle is smaller than the PTFE filter you use, (smallest siring filter pore size is 200nm) you can not separate them... I think.
are you sure that your synthesis method will yield monodisperse 8nm nanopartic;les?? may be thickness of shell on each core NPs are are not same (which you are predicting as aggregation). if the thickness of Shell on Core is thicker than the UV-vis abs will be dragged toward higher region (as the whole particle size will be increased).