After years of auditing plants a pattern repeats: the product does not fail on the obvious, but on an ingredient nobody looked at because it is a tiny fraction of the formula.
Gelatine and collagen derivatives
The classic. It appears in confectionery, dairy desserts, capsules, coatings and as a fining agent in beverages. Origin must be documented unambiguously; "food gelatine" on a data sheet says nothing.
Enzymes
Present in cheesemaking, baking, juices and alcohol-free brewing. The question is not only the enzyme's origin but the culture medium and the processing aids used to produce it. This is where you most often have to go to the supplier's supplier.
Emulsifiers, stearates and technical fats
E-471, E-472 and family can be of plant or animal origin, and the data sheet rarely clarifies which. The same goes for antifoams and release agents.
Flavourings and extracts
The flavour itself may be suitable, but the carrier may not. Ethanol as a solvent is common, and data sheets often list it simply as "carrier". It is one of the points that delays files most.
Colourants
Carmine (E-120) is animal-derived. Some colourants are stabilised with fat-based carriers that need verifying.
Technical alcohol
As an extraction solvent, cleaning agent or vehicle. Its treatment depends on the standard and the use, but it always has to be declared and quantified.
How to tackle it
Build a table with each ingredient, its E number if it has one, the supplier, the declared origin and whether a valid halal certificate exists. Flag in red anything you cannot document. That red list is, in practice, your work plan: resolving it before opening the file turns a one-year certification into a three-month one.