"[My merits] have become small" [Vayishlach 32:11]
When G-d shows His kindness to a person, it brings that person closer to G-d, causing his feeling of self-importance to diminish, since "everything is like nothing before G-d".
Therefore, it was precisely due to the fact that G-d had been so kind to Yaakov that he became small in his own eyes - for the kindness brought him closer to G-d, and so he felt that he was not worthy of G-d's promise to be saved.
Source: based on Tanya Igeres Hakodesh ch.2
How could Yaakov the patriarch fear that "perhaps... I have become soiled with sin" [Rashi v. 12] when surely he was aware that he had not sinned?
A tzadik is not static - he constantly grows spiritually from one level to the next. After reaching a higher level, his previous actions are spiritually deficient compared to his current standing. They are thus considered as "sins", metaphorically speaking. [The Hebrew word for sin - chet - can also mean ''deficiency'' [see Kings 11:21] Thus Yaakov was worried that perhaps due to such ''sins'' he was not worthy to be saved.
Source: based on Likutei Sichos Lubavitcher Rebbe