They should have told you why in the rejection letter. In addition, you can always request the GCMS notes (see http://www.cic.gc.ca/english/department/atip/form-imm5563.asp for the forms, but you must use someone in Canada to order them. If you don't know anyone there, you can use a commercial service to order them for you.) However, it seems likely that they believed your spouse was likely not to leave the country at the end of the TRV.
If you have a PR application submitted and a TRV is rejected because they don't believe your spouse is going to leave, you can also request a Temporary Resident Permit (TRP) under the "early admission" category (see OP 20 "Temporary Resident Permits"). There is a $200 fee for a TRP application and their grant is entirely discretionary. But pending spousal sponsorship applications in which everything looks good are exactly the category that should be granted.
It is absolutely not true that you cannot obtain a work permit or TRV with an in-process application. Search for "dual intent" on the CIC website. I obtained my first work permit while my FSW application was pending and had no problems doing so. However, you have to be able to convince CIC that you will leave at the end of the process. As I noted before, if their only grounds for rejecting a TRV application is a fear of overstay, you can apply for a TRP with a pending family PR application. However, with a intra-company transfer, I would be rather surprised for them to reject a work permit application - it's possible, but not likely.
Good luck!