Spouse visa

My japanese wife is applying me for spouse visa to be with her in Japan.My wife already passed all the documents that immigration needed.
After few days immigartion sent a letter about my past visa application that has been denied this january2017.

Actually I was a trainee visa for 3 years (2011-2014)in Japan.and after my contract finished my company wants to rehire me so they contacted me.

October 2016 my company introduce me to coordinate to a company named (company A)then this company processed my visa application but it was deny this January 2017

The problem is The letter I have sent to immigration about my denied visa application was not matched from what the (company A) applied for..
I have no knowledge that company A wanted to hire me in their company
I only know that my old company will rehire me and Company A will only assists me for my working visa application
Luckily I also included all the email conversation with Company A to immigration to testify that I am saying a true statement in my letter
and I also sent my certification of employment as trainee..

My question is
Do it affects my spouse visa application?
Even though my letter doesnt matched from what company A applied for me and I just stated the knowledge I know about my denied working visa?

You've stated the facts honestly, so it should be OK. You didn't know what the company A did/said.

However, having had your work visa denied as recently as January of this year raises the suspicion in the mind of immigration officers that you might have gotten married (I don't know when your marriage took place) for the primary purpose of being able to work in Japan on the "spouse of Japanese national" status. Therefore, I would not be surprised even if they asked extensive questions about the relationship with your wife - how you met, how many times you've been to Japan/she's been to your country, etc.

Updated

Actually me and my wife is having an coversation since 2015 and then in relationship since 2016 and living with me here in the Philippines about 6-8 months before my working visa get denied hence january 2017
And get married july this year in Philippines.
The good thing was my wife included all our photos, the first day we met, and all the adventure we have done in the philippines with dates captured by phone.
Do you think immigration will approve my coe?

Actually I and my wife is having an coversation since 2015 and then in relationship since 2016 before my working visa get denied hence january 2017
And get married july this year.
The good thing was my wife included our photos since we have met in the philippines with date that she captured by phone.
Do you think immigration will approve my coe?

Actually I and my wife is having an coversation since 2015 and then in relationship since 2016 before my working visa get denied hence january 2017
And get married july this year.
The good thing was my wife included our photos since we have met in the philippines with date that she captured by phone.
Do you think immigration will approve my coe?

Please stop updating with the same information.

Your relationship is since 2015, and you have papers to show that.
Your work visa got denied in January 2017, and you got married July 2017.
It is likely to "look as if" you got married to come work in Japan, so immigration authorities might ask more questions and ask further about your finance and things like that.

Once they are convinced that the marriage is genuine and that you (the two of you) have sufficient means to support your living, it will be granted, as far as I know. Just be ready for questions and a bit lengthy review time.

But I am not an immigration officer: it is up to them to make the decision.