You could brominate the acetophenone (base and bromine) and make a stabilised Wittig ylid with triphenylphosphine and base. The Wittig Ylid should react with a heterocyclic Aldehyde even if the heterocycle is a bit acidic (e.g. an indole or if a heteroatom e.g. NH or OH is reacting with the Ketone in the acetophenone when you try your Aldol),

see Clayden, Greeves, Warren, Wothers, Organic Chemistry, OUP,  2001, p700

If you react the heterocyclic Aldehyde with CH2=PPh3 and use it 1-phenylprop-2-enone (PhCOCH=CH2))  with Grubbs II you could make Chalcones by cross Metathesis.see Z. Gan R. Roy Tetrahedron, 2000, 56, p1423.

A few thoughts:

1. The base catalyze do Aldol is reversible

2. In the presence of base the aldehyde could be doing a Cannizzaro RX

3. In the presence of base the aldehyde could be doing a benzoin condensation

I would recommend you to use this procedure:

Org. Synth. 1922, 2, 1

DOI: 10.15227/orgsyn.002.0001

and increase the reaction time in the case of elrctron-rich heterocyclic aldehydes.

http://www.orgsyn.org/demo.aspx?prep=CV1P0078

I agree with Prof Heirtzier in that the type of heterocyclic aldehyde together with the base used are deceicive ion such reactions

There are several reports on chalcones prepared using heterocyclic aldehydes using the methods described in organic synthesis. They report yields above 70%. You can look into reaxys as it has lot of references which might be useful to you. However I am not sure if the reaction for aldehyde you need is available. 

You can try stirring ketone in base for about 20-30 min to generate anion and then slowly add your heterocyclic aldehyde dissolved in solvent. 

Good luck

Thanks Vathan