Sorry, forgot to list the relevant org-mode faces that I have customized:

First one is `org-block-begin-line'

Family: unspecified
Foundry: unspecified
Width: unspecified
Height: unspecified
Weight: unspecified
Slant: italic
Foreground: #969896
DistantForeground: unspecified
Background: #373b41
Underline: t
Overline: unspecified
Strike-through: unspecified
Box: unspecified
Inverse: unspecified
Stipple: unspecified
Font: unspecified
Fontset: unspecified
Inherit: unspecified

Second one is `org-block-end-line'

Family: unspecified
Foundry: unspecified
Width: unspecified
Height: unspecified
Weight: unspecified
Slant: italic
Foreground: #969896
DistantForeground: unspecified
Background: #373b41
Underline: unspecified
Overline: t
Strike-through: unspecified
Box: unspecified
Inverse: unspecified
Stipple: unspecified
Font: unspecified
Fontset: unspecified
Inherit: unspecified

Please note that this is not relevant to only Org mode, this display bug
happens with all faces
where I turn on the overline or underline property. For example
`font-lock-comment-face' will show
the same bug if I turn on the overline or underline property.