The first thing to point out here is that you are referring to media directed at the general public, not scientific publications. "Science" article in newspapers and magazines are rarely objective and most of the time fail to convey the actual conclusion of the paper they cite.
This can be harmful to the public's perception of research results in many ways and I get upset by it quite often. Scientists themselves almost never write to the newspaper to correct false conclusions made from their work, not even when their own words are misinterpreted, taken out of context, or simply made up.
Is it true that some research today are manipulated to suit corporate
agenda particularly private funded?
It has been shown that, even with rigorous methodology, researchers will have a tendency to make companies that pays them happy. Note that this is not restricted to privately-funded research. Government agencies that fund research obviously also have agendas and are generally far more powerful than the average commercial company (the US Department of Defense comes to mind). There is also a 'scientifically correct' among public funding agencies and scientist throughout history have struggled when their findings conflicted with popular political opinions.
In general, what diminishes this effect is when a lot of people from various places and with competing or opposite interests are researching on the same topic. One can expect the biases to level themselves out.
Is there a way to identify commercial research?
Yes. First, read actual scientific literature and not lay articles in men's health or gossip magazines. Second, reputable journals always ask authors to state every source of funding, and possible conflicts of interest. Third, switch your brain on when you read and use your judgment. If one lone article by Smith J. et al. states that products manufactured by Smith J. LLC are the next big thing, use extra scrutiny.