You should have read the FAQ thread — Why don’t my fonts look good at small sizes?
It is due to lack of hinting. The original e is hinted, the Polish ę ogonek is unhinted. To fix it, which is a better solution anyway as it makes the font smaller and easier to edit, use composite glyphs.
Right-click in the ę ogonek glyph and select “Complete composites.” Or, select all of the new ogonek glyphs with Ctrl + Click and create the composites all at once.
Complete Composites Ogonek.png
But first, check that your font contains the Ogonek accent glyph (02DB hex or 731 decimal). If it doesn’t you will need to create it. This new glyph will still be unhinted, but the composites will use the hinted base glyphs, so will probably look good enough at small sizes.
If you’re using the Home Edition, complete composites is not available. To create composites in the Home Edition, select the two glyphs — e and ogonek accent — in the glyph overview and copy them to the clipboard. Open the glyph edit window for e ogonek and paste the clipboard contents to create a composite glyph.
Either way, you may need to adjust the position of the accent to suit the font design.
Adjust Position.png