Ash's instructions were awfully specific especially if the company had no idea what was there. I believe they kew what was there because of how specific Ash's instructions were from them.
Like SM says, they're really not all that specific, beyond knowing an organism was involved. We don't even know if the company figured out it was a warning or not, but given Ripley's sit-back-and-let-it-happen ease with translation, it seems likely they did.
The bottom line is, if you think the company knew more than the very basics ahead of time, you have to come up with a reason for why they didn't at least just restaff and retrofit a commercial vessel, if not send in a specialised ship (the absence of doing so is even more glaring after 'Prometheus
'). To this day, I've never seen anyone able to plausibly square that circle.