In my opinion the problems lies in the following often being the case:

1) Management using one team as a leverage against the other (usually in both directions)

2) A lack of understanding of the issues facing the other team (again in both directions)

3) No scope allowed to cater for the other team (often management favours one team but which one varies)

4) Poor skills (if someone isn't good at their own job then don't expect them to even try to understand yours - also applicable to both)

5) Job protection (same for all)

The problem lies in that we often work in environments where competition for resources is fierce so we would be naive to think that it doesn't permeate throughout. Better organisations try to avoid this by attempting to make all internal competition fair and based on the underlying principle that what is selected should be what is best for the organisation overall (including all its stakeholders).