I know no Latin, but playing around with Google Translate I came up with "Non insectum opus est". Insectum seems like a good stand in for a generic bug, but maybe blatta is better (see http://www.catb.org/jargon/html/B/bug.html)? And opus carries the connotation that the entire program is as designed.
Google Translate is unreliable with Latin and you should not take anything it gives seriously. The suggestion non insectum opus est sounds like "an insect is not work".
I am not aware of good Latin words for "bug" or "feature". Therefore I would take a different approach and suggest:
Non forte sed ratione.
Not by chance but by design.
Another option is to go with participles:
Non ruptum sed designatum.
Not broken but designed.
If you refer to something specific, remember that the Latin participle needs the correct form (gender and number). As just a general rule without referring to any single thing, I think singular neuter works well.
You can also substitute erratum (misstep, mistake) for ruptum (broken). This should be seen as a noun (errare is intransitive, so erratum is best seen as a derived noun rather than a participle). If you want to shift nuance from "broken" to "misstep", you can say Non erratum sed designatum.