See the light

Here: being left means someone right now is putting the bicycle there. So better: had been left/ or left (adj.)

Even better is to leave this out: I saw my bicycle under a tree. 

As I was approaching it, I became aware that it's   its saddle was fixed positioned higher than I expected.

I was disappointed that someone might have used my bicycle without my permission during my short prayer.

For me it looked slightly complicated/ tricky complex to restore  fix the saddle and I was in a hurry, so I left the saddle as it was and pushed my bicycle to the bakery.

to go to a bakery while pushing the bicycle.

Complex- more of a literary adjective. I wouldn't use it to describe this action. 

The sentence had become too complex with ´to go to a bakery´, and it also sounded like the 'subject' was unclear (who is going to the bakery? the saddle?) 

However again, in front of the bakery, I felt impatient as I found that I was not able to remember how to use its lock.

I left the bicycle unlocked and went into the shop while feeling that something mystifying had happened.

I went out the bakery a I left the bakery and I saw the bicycle standing in front of the shop.
As I was approaching it, a new idea came to me; to assume that that bicycle was not mine.

That idea resolved all my doubts.
Then, the more I looked at it the more of a stranger to me it looked to me.

better: the more strange/unfamiliar (adj.) it looked to me.

I had to go to church again to confess. :-(

Interesting and funny story. Good use of tenses for the most part. Well done.