Most important thing is to know where you are in a bar. Know Where beat one is first and foremost. It's actually what dictates how the music is written down - it tells how many beats are in each bar, it's usually the most emphasised bit of most bars.
For now, you're going to have to count. Nothing childish about that. Without knowing where 'one' is, nothing's going to improve.
For now, at least, consider each and every fill is going to finish on 'one'. So, if it's a short two beat fill, of, say, 4 quavers, it'll happen on 3-4 of a bar, and end with (probably) a chord tone on beat one of the next bar. Bear in mind that fills are most effective at the end of a line of singing (to let the vocalist have time to grab a breath!), so during bar 4 is a good fill time. As a bass player and drummer, it's the break I'm waiting for - literally!
Once you've got beat one sorted, try listening carefully to lots of songs, and establish what beat each part of the song starts on. It might be the anacrucis last beat of the bar. '1-2- Happy- birthday-to-you, or 1-2-3-On-Ilkeley - Moor - bah - Tat. By listening (and still counting), you'll have a greater awareness of where everything is in each bar - and each line.
A loop station is a great toy to help here. Play something simple, and practise playing fills over it. By the way, drummers don't play fills naturally by any means. One of my students plays some nice fills, but we're having an awful job timing them so they finish at the right time. At present, in 4/4 time, whenever there's a fill, there's a bar of 5/4. Not good for dancing to! So, you're not alone!