I have wooden window frames all around my house and some of them have knots in the windowledge. In the past these have been stripped down to bare wood using different methods over time ( heat gun, chemical etc) and treated with Knotting solution and then painted with exterior wood stain (Recently Johnstones - trade woodworks - satin woodstain but used other makes in the past). Usually within 6-12 months these knots have bubbled up and oozed the sap from the knots. I think the last painter used Rustins, but thats a guess. Is there a more permanent fix without changing the windows....
Yep, Guttercat is giving you good advice if you want a permanent solution. Don't stop the holes with a stopping or filler which contains oil. Use an appropriate water mixed filler or a two pack catalyst type or similar. If you cut out any large knots or you want to re-stain this wood then it may be best to plug the holes with sound wood, but greater skill is required.