This if-clause is not a conditional clause; it is instead an interrogative clause. The grammatical tense is the simple past because tense agreement requires the past. In sentences involving a conditional clause there is always expressed in the matrix clause a situation that should or should not be realized if the condition were to obtain.
(CoGEL § 15.33)
The central uses of conditional clauses express a DIRECT CONDITION: they
convey that the situation in the matrix clause is directly contingent on that of the conditional clause. Put another way, the truth of the proposition in the
matrix clause is a consequence of the fulfilment of the condition in the
conditional clause. Here is an example:
- If you put the baby down, she'll scream. [1]
In uttering [1] the speaker intends the hearer to understand that the truth of the prediction 'she'll scream' depends on the fulfilment of the condition of
'your putting the baby down'.
There is no such relation between the verbs in the OP's sentence.
In a situation where question concerns a present case of "going bad" we would have the following sentence, where the present is used naturally in the if nominal alternative interrogative clause (constructed with "whether …or" and "if … or; "if the batch was going bad because of the temperature or because of contamination").
- We are wondering if the batch is going bad because of the temperature or because of contamination.
If the asking of the question is about a "going bad" in the past, then the past is used.
- We are wondering if the batch was going bad because of the temperature or because of contamination.
Note: "Would" does not express the subjunctive, but simply an action in the past that was habitual or recurring.