I was confused about Form 5472 reportable transactions for domestic related parties.

Reporting corporation (RC):

Foreign Corp or

25% foreign owned.

Once you identified your corp. as a RC, the general rule applies:

Generally, a reporting corporation must file Form 5472 if it had a reportable  transaction with a foreign or domestic related party.

NOTE the specific "exception from filing" #1: (For other exceptions, you're on your own.) 

Exceptions from filing. A reporting corporation is not required to file Form
5472 if any of the following apply. 

1. It had no reportable transactions of the types listed in Parts IV and VI of the
form.

Therefore, if the RC did NOT have any of the Part IV or VI transactions with a foreign or domestic related party, NO F5472.

If the RC HAD any of the Part IV or VI transactions with a foreign or domestic related party, File F5472.

However, if the Part IV or VI transactions were with a DOMESTIC related party, file F5472 but the info of the transactions is NOT required in Part IV or VI.   That is, you have to disclose the info in other Parts of F5472, just that Part IV or VI would include only info for transactions with foreign related party(ies). 

Thus, if 100% of such transactions were with a DOMESTIC related party(ies), Part IV and VI would be blank.

This is based on the instructions under "Reportable transaction", which you cited:

Transactions with a U.S. related party, however, are not required to be specifically identified in Parts IV and VI.

Specifically addressing your questions:

I.  Regarding I feel like form 5472 has contradictions regarding the reportable transactions. 

Per form 5472 :"every reporting corporation must file a Form 5472 if it had a reportable transaction with a foreign or domestic related party"

Also per 5472:"Transactions with a U.S. related party, however, are not required to be specifically identified in Parts IV and VI" 

Joshua barkth: The former is the General rule specifying who must file.  The latter is a specific rule for whether the info for transaction with DOMESTIC DUDES has to be identified in Part IV and IV. 

A bit convoluted yes.  Contradiction no.

II.     I'm little confused about the language,  do I need to file 5472 if there is a transactions between a reporting company and it's domestic relate party?

Joshua barkth: YES.  Just that the info with the DOMESTIC DUDES does NOT need to be identified in Parts IV and VI.

III.   Also, for example , if a foreigner has 2 C Corps in US, they have some transactions between each other.  Do I need to file a form 5472 for each of them?

Joshua barkth:

YES.

NO need to put the info on the transactions between the two DOMESTIC C corps in Part IV or Part VI.

If either DOMESTIC C corp had transactions with the foreign dude or the applicable foreign entities controlled/owned by the foreign dude, report the info of the transactions on Part IV and/or Part VI.

Hope this helps.