A quick Google search suggests INDRA is a company "providing proprietary solutions in specific segments in Transport and Defence markets, and the leading firm in Digital Transformation Consultancy and Information Technologies".
Since Plus Valía is (usually, as far as I know) payable direct to the town hall, why would such an organisation be involved?
The "federal" tax you refer to is presumably the 3% retention - which would (usually) be retained by the buyer and submitted direct to Hacienda (the "federal treasury"). The notary would not (usually) get involved in any such transactions.
So, if as you say, the notary deducted (or retained) part of the sale proceeds in lieu of these charges, perhaps you need to start there, and find out why the money supposedly went to INDRA and not the town hall.
Other than that, I can't really offer any other suggestions.