More an observation than an answer (I post it here because I cannot put figures in comments). The behaviour seems to be caused by the Dashed attribute, and it is the line, not the point, that is not drawn correctly.
Op's code for me (v11.0.1 x64 on Windows 10) produces
point1 = {57.7538, 44.0056}; point2 = {57.7607, 43.9983}; line1 = Line[{point1, point2}]; line2 = Line[{{54.3101, 40.715}, {58.4058, 44.624}}]; intersectionPoint = First[{x, y} /. FindInstance[{x, y} ∈ line1 && {x, y} ∈ line2, {x, y}]]; Graphics[{ {Gray, line1}, {PointSize[Large], Point[{point1, point2}]}, {PointSize[Large], Red, Point[intersectionPoint]} }, Prolog -> {Dashed, line2}, Frame -> True, ImageSize -> Large ]

Removing the Dashed attribute in the Prolog option, I get:
point1 = {57.7538, 44.0056}; point2 = {57.7607, 43.9983}; line1 = Line[{point1, point2}]; line2 = Line[{{54.3101, 40.715}, {58.4058, 44.624}}]; intersectionPoint = First[{x, y} /. FindInstance[{x, y} ∈ line1 && {x, y} ∈ line2, {x, y}]]; Graphics[{ {Gray, line1}, {PointSize[Large], Point[{point1, point2}]}, {PointSize[Large], Red, Point[intersectionPoint]} }, Prolog -> {line2}, Frame -> True, ImageSize -> Large ]

Drawing line2 inside the same Graphics as the rest of the objects doesn't change this, so it doesn't look like a problem in Prolog.
Even better, the lower the Dashing, the further away the line is drawn from the intersection point:
point1 = {57.7538, 44.0056}; point2 = {57.7607, 43.9983}; line1 = Line[{point1, point2}]; line2 = Line[{{54.3101, 40.715}, {58.4058, 44.624}}]; intersectionPoint = First[{x, y} /. FindInstance[{x, y} ∈ line1 && {x, y} ∈ line2, {x, y}]]; Graphics[{ {Gray, line1}, {PointSize[Large], Point[{point1, point2}]}, {PointSize[Large], Red, Point[intersectionPoint]} }, Prolog -> Map[{Hue[10 #], Dashing@#, line2} &]@Range[0, .5, 0.01], Frame -> True, ImageSize -> Large ]

I have no idea why this happens.
Dashedit shows correctly $\endgroup$