If a company that your interested in promoting states that they also promote with ppc themselves, does that put you off in any way as an affiliate?
Ask them. They should tell you what they allow. Some may restrict you from a certain service, such as adwords, but I find it is more common to see those that promote their own product through ppc to specify both a service and a specific list of keywords that they do not want you touching and leave you free to all the rest.
NO, This is just a common thing and you can encounter this on any affiliate program that you join. Just study your keywords very well.