I realise I did not give some time for the chemicals (which are releasing heat during an exothermic reaction) to cool down first and instead, I added another chemical substance to the reaction mixture immediately. Is it a red flag that I might lose some of my products and get a lower percentage yield? The experiment that I will be doing is Jacobsen's ligand asymmetric synthesis.
It depends on the reaction, some are more temperature sensitive than others. You might get a slightly reduced yield or, at the other end of the spectrum, a runaway reaction leading to a redecorated fumehood.
For the Jacobsen asymmetric epoxidation this quote from the Wikipedia article here seems relevant:
The degree of enantioselectivity depends on numerous factors, namely the structure of the alkene, the nature of the axial donor ligand on the active oxomanganese species and the reaction temperature.
So at the least you'll get reduced enantioselectivity. For other reactions (e.g. lithium-halogen exchange) getting the temperature wrong can generate completely different products than the one you were trying for.