Firstly, you do need to have some realistic expectations about desktop 3d printing accuracy.

Here are a few ways to reduce this error, although others may also have better suggestions.

1. try increasing the hole size to account for this error in your design software.
2. if you reduce the nozzle size then you will increase your xy resolution, this will reduce the error introduced by your path thickness.
3. Increasing layer height will also reduce path thickness i.e. tall and thin as opposed to short and fat exudate path.